From ca4aafa34d79124e078b0175a66d0ff050a69b94 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 6 May 2024 17:34:41 +1000
Subject: [PATCH 1/8] devtools check/styler - part1

---
 R/purple.R                                    | 80 +++++++++----------
 R/sv.R                                        | 36 ++++-----
 R/umccrise.R                                  |  2 +-
 man/cancer_rmd.Rd                             |  1 +
 man/purple_cnv_som_gene_process.Rd            |  4 +-
 .../test-roxytest-testexamples-purple.R       |  8 +-
 6 files changed, 64 insertions(+), 67 deletions(-)

diff --git a/R/purple.R b/R/purple.R
index 713e20c..5881d70 100644
--- a/R/purple.R
+++ b/R/purple.R
@@ -124,7 +124,6 @@ purple_cnv_som_gene_process <- function(x, g = NULL) {
 }
 
 sash_read_cnv_tsv <- function(x) {
-
   nm <- c(
     "chromosome" = "c",
     "start" = "i",
@@ -152,7 +151,6 @@ sash_read_cnv_tsv <- function(x) {
 }
 
 filter_and_split_annotations_cnv <- function(x) {
-
   filter_conditions <- list(
     # Chromosome effects
     stringr::str_starts(x$Detail, "chrom_"),
@@ -162,34 +160,34 @@ filter_and_split_annotations_cnv <- function(x) {
 
   x.grouped <- x |>
     dplyr::group_by(
-      filter=ifelse(purrr::reduce(filter_conditions, `|`), "filter", "retain")
+      filter = ifelse(purrr::reduce(filter_conditions, `|`), "filter", "retain")
     )
 
   keys <- x.grouped |>
     dplyr::group_keys() |>
-    dplyr::pull(filter)
+    dplyr::pull("filter")
 
   x.split <- x.grouped |>
-    dplyr::group_split(.keep=FALSE) |>
+    dplyr::group_split(.keep = FALSE) |>
     purrr::set_names(keys)
 
   list(
     retained = purrr::pluck(x.split, "retain"),
-    filtered = purrr::pluck(x.split, "filter") |> dplyr::arrange(Tier, `Event ID`)
+    filtered = purrr::pluck(x.split, "filter") |> dplyr::arrange("Tier", "Event ID")
   )
 }
 
 collapse_effect_group <- function(x) {
   x.tmp <- dplyr::first(x)
   genes <- x.tmp |>
-    dplyr::pull(Genes.unique) |>
+    dplyr::pull("Genes.unique") |>
     unlist()
 
   x.tmp |>
     dplyr::mutate(
-      Genes = paste0(genes, collapse=", "),
+      Genes = paste0(genes, collapse = ", "),
       Transcripts = "",
-      Detail = paste0(unique(x$Detail) |> sort(), collapse=", "),
+      Detail = paste0(unique(x$Detail) |> sort(), collapse = ", "),
       Tier = min(x$Tier),
       `Annotation ID` = NA,
     )
@@ -201,16 +199,16 @@ set_many_genes_cnv <- function(x) {
   x.counts <- x |>
     dplyr::group_by(`Event ID`, Effect) |>
     dplyr::mutate(
-      Genes.unique = Genes |> stringr::str_split(", ") |> unlist() |> unique() |> list(),
-      `Gene count (effect group)` = Genes.unique |> dplyr::first() |> length(),
-      collapse = `Gene count (effect group)` > 2 & Effect %in% collapse_effects,
+      Genes.unique = .data$Genes |> stringr::str_split(", ") |> unlist() |> unique() |> list(),
+      `Gene count (effect group)` = .data$Genes.unique |> dplyr::first() |> length(),
+      collapse = .data$`Gene count (effect group)` > 2 & .data$Effect %in% collapse_effects,
     ) |>
-    dplyr::select(-`Gene count (effect group)`)
+    dplyr::select(-"Gene count (effect group)")
 
   # Collapse target groups
   x.collapsed <- x.counts |>
     dplyr::filter(collapse) |>
-    dplyr::select(-collapse) |>
+    dplyr::select(-"collapse") |>
     dplyr::group_modify(~ collapse_effect_group(.x)) |>
     # Update top tier, referring to complete data set within each group
     dplyr::mutate(
@@ -226,7 +224,7 @@ set_many_genes_cnv <- function(x) {
   x.tmp <- x.counts |>
     dplyr::filter(!collapse) |>
     dplyr::bind_rows(x.collapsed) |>
-    dplyr::select(-c(collapse, Genes.unique, Tier)) |>
+    dplyr::select(-c("collapse", "Genes.unique", "Tier")) |>
     dplyr::rowwise() |>
     dplyr::mutate(
       `Gene count` = Genes |> stringr::str_split(", ") |> unlist() |> unique() |> length(),
@@ -267,7 +265,7 @@ set_many_genes_cnv <- function(x) {
       ),
       Transcripts = ifelse(many_genes == "few_genes" | is.na(many_genes), Transcripts, ""),
     ) |>
-    dplyr::select(-c(many_genes, `Gene count`))
+    dplyr::select(-c("many_genes", "Gene count"))
 
   list(
     ready = x.ready,
@@ -314,7 +312,7 @@ set_many_transcripts_cnv <- function(x) {
         paste0("Many transcripts (", `Transcript count`, ")")
       )
     ) |>
-    dplyr::select(-c(many_transcripts, `Transcript count`))
+    dplyr::select(-c("many_transcripts", "Transcript count"))
 
   list(
     ready = x.ready,
@@ -330,29 +328,27 @@ process_cnv_tsv <- function(x) {
   # Prepare input
   cnv.ready <- cnv.input |>
     dplyr::mutate(
-      chrom_simple = stringr::str_remove(chromosome, "chr"),
-      start = paste(chrom_simple, base::format(start, big.mark = ",", trim = TRUE), sep=":"),
-      end = paste(chrom_simple, base::format(end, big.mark = ",", trim = TRUE), sep=":"),
+      chrom_simple = stringr::str_remove(.data$chromosome, "chr"),
+      start = paste(.data$chrom_simple, base::format(.data$start, big.mark = ",", trim = TRUE), sep = ":"),
+      end = paste(.data$chrom_simple, base::format(.data$end, big.mark = ",", trim = TRUE), sep = ":"),
     ) |>
-    dplyr::select(-c(
-      chromosome,
-      chrom_simple,
-    ))
+    dplyr::select(-c("chromosome", "chrom_simple"))
 
   # Melt annotations
   cnv.tmp <- cnv.ready |>
     dplyr::mutate(`Event ID` = dplyr::row_number()) |>
     # Split into individual annotations
-    dplyr::mutate(annotation = strsplit(simple_ann, ",")) |>
+    dplyr::mutate(annotation = strsplit(.data$simple_ann, ",")) |>
     # Convert annotation fields into columns
-    tidyr::unnest(annotation) |>
+    tidyr::unnest("annotation") |>
     tidyr::separate(
-      annotation, c("Event", "Effect", "Genes", "Transcripts", "Detail", "Tier"),
+      "annotation",
+      c("Event", "Effect", "Genes", "Transcripts", "Detail", "Tier"),
       sep = "\\|", convert = FALSE
     ) |>
     # Create new columns and modify existing ones
     dplyr::mutate(
-      copyNumber = as.numeric(copyNumber) |> round(2) %>% sprintf("%.2f", .),
+      copyNumber = as.numeric(.data$copyNumber) |> round(2) %>% sprintf("%.2f", .),
       minorAlleleCopyNumber = as.numeric(minorAlleleCopyNumber) |> round(2) %>% sprintf("%.2f", .),
       majorAlleleCopyNumber = as.numeric(majorAlleleCopyNumber) |> round(2) %>% sprintf("%.2f", .),
       "PURPLE CN Min+Maj" = paste0(minorAlleleCopyNumber, "+", majorAlleleCopyNumber),
@@ -361,18 +357,18 @@ process_cnv_tsv <- function(x) {
     ) |>
     # Remove unused columns
     dplyr::select(-c(
-      baf,
-      bafCount,
-      depthWindowCount,
-      Event,
-      gcContent,
-      majorAlleleCopyNumber,
-      method,
-      minorAlleleCopyNumber,
-      segmentEndSupport,
-      segmentStartSupport,
-      sv_top_tier,
-      simple_ann,
+      "baf",
+      "bafCount",
+      "depthWindowCount",
+      "Event",
+      "gcContent",
+      "majorAlleleCopyNumber",
+      "method",
+      "minorAlleleCopyNumber",
+      "segmentEndSupport",
+      "segmentStartSupport",
+      "sv_top_tier",
+      "simple_ann",
     ))
 
   # Abbreviate effects
@@ -411,7 +407,7 @@ process_cnv_tsv <- function(x) {
     "PURPLE CN" = "copyNumber",
     "PURPLE CN Min+Maj"
   )
-  cnv.tmp <- dplyr::select(cnv.tmp, tidyselect::all_of(c(column_selector, "Tier")))
+  cnv.tmp <- dplyr::select("cnv.tmp", tidyselect::all_of(c(column_selector, "Tier")))
   cnv.filtered <- dplyr::select(cnv.annotations.split$filtered, tidyselect::any_of(column_selector))
 
   # Collapse selected annotations and set many genes
@@ -744,7 +740,7 @@ purple_kataegis <- function(x) {
 
   data <- d$data |>
     dplyr::filter(!is.na(.data$KT)) |>
-    dplyr::select(c("CHROM", "POS", info_cols))
+    dplyr::select(c("CHROM", "POS", tidyselect::all_of(info_cols)))
 
   description <- d$description |>
     dplyr::filter(.data$ID %in% info_cols) |>
diff --git a/R/sv.R b/R/sv.R
index 69df9ec..9afdda8 100644
--- a/R/sv.R
+++ b/R/sv.R
@@ -126,7 +126,6 @@ abbreviate_effect <- function(effects) {
 }
 
 sash_read_sv_tsv <- function(x) {
-
   tab <- dplyr::tribble(
     ~Column, ~Description, ~Type,
     "chrom", "CHROM column in VCF", "c",
@@ -162,11 +161,11 @@ sash_read_sv_tsv <- function(x) {
 }
 
 split_svs <- function(x) {
-  bps_types <-  c("BND", "DEL", "DUP"," INS", "INV")
+  bps_types <- c("BND", "DEL", "DUP", " INS", "INV")
 
   x.grouped <- x |>
     dplyr::group_by(
-      record_type=ifelse(Type %in% bps_types, "bps", "other")
+      record_type = ifelse(Type %in% bps_types, "bps", "other")
     )
 
   keys <- x.grouped |>
@@ -174,7 +173,7 @@ split_svs <- function(x) {
     dplyr::pull(record_type)
 
   x.split <- x.grouped |>
-    dplyr::group_split(.keep=FALSE) |>
+    dplyr::group_split(.keep = FALSE) |>
     purrr::set_names(keys)
 
   list(
@@ -186,8 +185,8 @@ split_svs <- function(x) {
 join_breakpoint_entries <- function(x) {
   # Group by GRIDSS identifier (clipping trailing h/o [h: High, o: lOwer])
   bps <- x |>
-    tidyr::separate(ID, into = c("BND_group", "BND_mate"), sep = -1, convert = TRUE, remove = FALSE)|>
-    dplyr::group_by(BND_group)
+    tidyr::separate("ID", into = c("BND_group", "BND_mate"), sep = -1, convert = TRUE, remove = FALSE) |>
+    dplyr::group_by("BND_group")
 
   # Set a sequential breakpoint identifier
   bps_groups <- bps |> dplyr::n_groups()
@@ -195,15 +194,17 @@ join_breakpoint_entries <- function(x) {
     dplyr::mutate(
       # Assign a unique ID based on current group
       BND_ID = sprintf(paste0("%0", nchar(bps_groups), "d"), dplyr::cur_group_id()),
-      BND_mate = ifelse(BND_mate == "o", "A", "B"),
+      BND_mate = ifelse(.data$BND_mate == "o", "A", "B"),
     ) |>
     dplyr::ungroup() |>
     dplyr::mutate(
-      end_position = sub("^.*:(\\d+).*$", "\\1", ALT) |> as.numeric() |> base::format(big.mark = ",", trim = TRUE),
-      end_chrom = sub("^.*chr(.*):.*$", "\\1", ALT),
-      end = paste0(end_chrom, ":", end_position),
+      end_position = sub("^.*:(\\d+).*$", "\\1", .data$ALT) |>
+        as.numeric() |>
+        base::format(big.mark = ",", trim = TRUE),
+      end_chrom = sub("^.*chr(.*):.*$", "\\1", .data$ALT),
+      end = paste0(.data$end_chrom, ":", .data$end_position),
     ) |>
-    dplyr::select(-c(end_position, end_chrom))
+    dplyr::select(-c("end_position", "end_chrom"))
 }
 
 remove_gene_fusion_dups <- function(.data, columns) {
@@ -211,7 +212,7 @@ remove_gene_fusion_dups <- function(.data, columns) {
   v.groups <- c("frameshift_variant&gene_fusion", "gene_fusion")
   v.effects_ordered <- sapply(.data$Effect, function(s) {
     c <- stringr::str_split(s, "&") |> unlist()
-    paste0(sort(c), collapse="&")
+    paste0(sort(c), collapse = "&")
   })
 
   if (all(v.groups %in% v.effects_ordered)) {
@@ -222,7 +223,6 @@ remove_gene_fusion_dups <- function(.data, columns) {
 }
 
 filter_and_split_annotations_sv <- function(x) {
-
   filter_conditions <- list(
     # Empty Gene field
     x$Genes == "",
@@ -236,16 +236,16 @@ filter_and_split_annotations_sv <- function(x) {
 
   x.grouped <- x |>
     dplyr::group_by(
-      filter=ifelse(purrr::reduce(filter_conditions, `|`), "filter", "retain")
+      filter = ifelse(purrr::reduce(filter_conditions, `|`), "filter", "retain")
     ) |>
-    dplyr::select(-c(Type, `Top Tier`))
+    dplyr::select(-c("Type", "Top Tier"))
 
   keys <- x.grouped |>
     dplyr::group_keys() |>
-    dplyr::pull(filter)
+    dplyr::pull("filter")
 
   x.split <- x.grouped |>
-    dplyr::group_split(.keep=FALSE) |>
+    dplyr::group_split(.keep = FALSE) |>
     purrr::set_names(keys)
 
   list(
@@ -325,7 +325,7 @@ process_sv <- function(x) {
         is.na(PR_asm_alt) ~ SR_asm_alt,
         .default = SR_asm_alt + PR_asm_alt,
       ),
-      start = paste(chrom, base::format(start, big.mark = ",", trim = TRUE), sep=":"),
+      start = paste(chrom, base::format(start, big.mark = ",", trim = TRUE), sep = ":"),
       Type = ifelse(is.na(PURPLE_status), svtype, "PURPLE_inf"),
       "Record ID" = dplyr::row_number(),
     ) |>
diff --git a/R/umccrise.R b/R/umccrise.R
index 1c81b27..4a5b212 100644
--- a/R/umccrise.R
+++ b/R/umccrise.R
@@ -26,7 +26,7 @@ bcftools_stats_plot <- function(x = NULL) {
     dplyr::select("qual", "snps", "indels") |>
     tidyr::uncount(.data$snps + .data$indels) |>
     dplyr::select("qual")
-  med <- median(d$qual, na.rm = TRUE)
+  med <- stats::median(d$qual, na.rm = TRUE)
   tot <- nrow(d)
   p <- d |>
     ggplot2::ggplot(ggplot2::aes(x = .data$qual)) +
diff --git a/man/cancer_rmd.Rd b/man/cancer_rmd.Rd
index ccc1012..e13b101 100644
--- a/man/cancer_rmd.Rd
+++ b/man/cancer_rmd.Rd
@@ -8,6 +8,7 @@ cancer_rmd(
   af_global,
   af_keygenes,
   batch_name,
+  bcftools_stats,
   conda_list,
   dragen_hrd,
   img_dir,
diff --git a/man/purple_cnv_som_gene_process.Rd b/man/purple_cnv_som_gene_process.Rd
index e5aaf00..a859cad 100644
--- a/man/purple_cnv_som_gene_process.Rd
+++ b/man/purple_cnv_som_gene_process.Rd
@@ -11,8 +11,8 @@ purple_cnv_som_gene_process(x, g = NULL)
 
 \item{g}{Path to gene file containing at least three columns:
 \itemize{
-\item \code{symbol}: gene name (character).
-\item \code{tumorsuppressor}: is this gene a tumor suppressor (TRUE/FALSE).
+\item \code{ensembl_gene_symbol}: gene name (character).
+\item \code{tsgene}: is this gene a tumor suppressor (TRUE/FALSE).
 \item \code{oncogene}: is this gene an oncogene (TRUE/FALSE).
 }}
 }
diff --git a/tests/testthat/test-roxytest-testexamples-purple.R b/tests/testthat/test-roxytest-testexamples-purple.R
index a9fde90..46bdedc 100644
--- a/tests/testthat/test-roxytest-testexamples-purple.R
+++ b/tests/testthat/test-roxytest-testexamples-purple.R
@@ -19,7 +19,7 @@ test_that("Function purple_cnv_som_gene_process() @ L60", {
 })
 
 
-test_that("Function purple_cnv_som_read() @ L449", {
+test_that("Function purple_cnv_som_read() @ L447", {
   
   x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
   (p <- purple_cnv_som_read(x))
@@ -27,7 +27,7 @@ test_that("Function purple_cnv_som_read() @ L449", {
 })
 
 
-test_that("Function purple_cnv_som_process() @ L482", {
+test_that("Function purple_cnv_som_process() @ L480", {
   
   x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
   (pp <- purple_cnv_som_process(x))
@@ -35,7 +35,7 @@ test_that("Function purple_cnv_som_process() @ L482", {
 })
 
 
-test_that("Function purple_qc_read() @ L550", {
+test_that("Function purple_qc_read() @ L548", {
   
   x <- system.file("extdata/purple/purple.qc", package = "gpgr")
   (q <- purple_qc_read(x))
@@ -43,7 +43,7 @@ test_that("Function purple_qc_read() @ L550", {
 })
 
 
-test_that("Function purple_purity_read() @ L608", {
+test_that("Function purple_purity_read() @ L606", {
   
   x <- system.file("extdata/purple/purple.purity.tsv", package = "gpgr")
   (p <- purple_purity_read(x))

From baf18147b66b099cd3289bd3a13eaebc8343e204 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 6 May 2024 18:36:46 +1000
Subject: [PATCH 2/8] devtools check/styler - part2

---
 R/oncokb.R                                    |  8 +-
 R/purple.R                                    | 46 +++++------
 R/sv.R                                        | 80 +++++++++----------
 R/umccrise.R                                  |  2 +-
 .../test-roxytest-testexamples-purple.R       |  8 +-
 5 files changed, 73 insertions(+), 71 deletions(-)

diff --git a/R/oncokb.R b/R/oncokb.R
index 03954aa..8f3963f 100644
--- a/R/oncokb.R
+++ b/R/oncokb.R
@@ -2,7 +2,7 @@
 read_oncokb <- function(x) {
   readr::read_tsv(x) |>
     dplyr::filter(
-      `OncoKB Annotated` == "Yes"
+      .data$`OncoKB Annotated` == "Yes"
     ) |>
     dplyr::pull("Hugo Symbol")
 }
@@ -16,9 +16,11 @@ get_oncokb_genes <- function(x, oncokb_genes) {
     # Create regexes for each match, utilising delimiters for boundaries. Handles most cases where a gene symbol contains the '-' delimiter
     purrr::map(function(n) paste0("(?<=^|", delimiter_re, ")", n, "(?=", delimiter_re, "|$)")) |>
     # Loop with nm iterations through regex and gene symbols
-    purrr::map(function(n) stringr::str_detect(x, n) |> tibble::as_tibble_row(.name_repair="unique_quiet")) |>
+    purrr::map(function(n) stringr::str_detect(x, n) |> tibble::as_tibble_row(.name_repair = "unique_quiet")) |>
     # Combine as tibble to access dplyr::summarise and compile list of detected OncoKB gene symbols for each effect
     dplyr::bind_rows() |>
-    dplyr::summarise(dplyr::across(dplyr::everything(), function(v) { paste0(sort(oncokb_genes[v]), collapse=", ") })) |>
+    dplyr::summarise(dplyr::across(dplyr::everything(), function(v) {
+      paste0(sort(oncokb_genes[v]), collapse = ", ")
+    })) |>
     unlist()
 }
diff --git a/R/purple.R b/R/purple.R
index 5881d70..6a7fbbe 100644
--- a/R/purple.R
+++ b/R/purple.R
@@ -173,7 +173,7 @@ filter_and_split_annotations_cnv <- function(x) {
 
   list(
     retained = purrr::pluck(x.split, "retain"),
-    filtered = purrr::pluck(x.split, "filter") |> dplyr::arrange("Tier", "Event ID")
+    filtered = purrr::pluck(x.split, "filter") |> dplyr::arrange(.data$Tier, .data$`Event ID`)
   )
 }
 
@@ -197,7 +197,7 @@ set_many_genes_cnv <- function(x) {
   # Count genes and set eligibility for collapsing
   collapse_effects <- c("DelG", "Dup", "DelTx", "UpstreamGV", "DnstreamGV", "IntergenReg")
   x.counts <- x |>
-    dplyr::group_by(`Event ID`, Effect) |>
+    dplyr::group_by(.data$`Event ID`, .data$Effect) |>
     dplyr::mutate(
       Genes.unique = .data$Genes |> stringr::str_split(", ") |> unlist() |> unique() |> list(),
       `Gene count (effect group)` = .data$Genes.unique |> dplyr::first() |> length(),
@@ -207,12 +207,12 @@ set_many_genes_cnv <- function(x) {
 
   # Collapse target groups
   x.collapsed <- x.counts |>
-    dplyr::filter(collapse) |>
+    dplyr::filter(.data$collapse) |>
     dplyr::select(-"collapse") |>
     dplyr::group_modify(~ collapse_effect_group(.x)) |>
     # Update top tier, referring to complete data set within each group
     dplyr::mutate(
-      `Tier (top)` = paste0(Tier, " (", min(x$Tier[x$`Event ID` == `Event ID`]), ")"),
+      `Tier (top)` = paste0(.data$Tier, " (", min(x$Tier[x$`Event ID` == .data$`Event ID`]), ")"),
     ) |>
     # Create new annotation ID
     dplyr::ungroup() |>
@@ -222,26 +222,26 @@ set_many_genes_cnv <- function(x) {
 
   # Bind collapsed rows with uncollapsed rows, then count genes per entry
   x.tmp <- x.counts |>
-    dplyr::filter(!collapse) |>
+    dplyr::filter(!.data$collapse) |>
     dplyr::bind_rows(x.collapsed) |>
     dplyr::select(-c("collapse", "Genes.unique", "Tier")) |>
     dplyr::rowwise() |>
     dplyr::mutate(
-      `Gene count` = Genes |> stringr::str_split(", ") |> unlist() |> unique() |> length(),
+      `Gene count` = .data$Genes |> stringr::str_split(", ") |> unlist() |> unique() |> length(),
     ) |>
     dplyr::ungroup() |>
     # Sort rows
-    dplyr::arrange(`Tier (top)`, `Event ID`)
+    dplyr::arrange(.data$`Tier (top)`, .data$`Event ID`)
 
   # Set many genes
   x.tmp <- x.tmp |>
     dplyr::mutate(
-      many_genes = ifelse(`Gene count` > 2, "many_genes", "few_genes"),
+      many_genes = ifelse(.data$`Gene count` > 2, "many_genes", "few_genes"),
     )
 
   # Build the many genes table
   x.many_genes <- x.tmp |>
-    dplyr::filter(many_genes == "many_genes") |>
+    dplyr::filter(.data$many_genes == "many_genes") |>
     # Remove unneeded columns and rename others
     dplyr::select(
       "Event ID",
@@ -259,11 +259,11 @@ set_many_genes_cnv <- function(x) {
   x.ready <- x.tmp |>
     dplyr::mutate(
       Genes = ifelse(
-        many_genes == "few_genes" | is.na(many_genes),
-        Genes,
-        paste0("Many genes (", `Gene count`, ")")
+        .data$many_genes == "few_genes" | is.na(.data$many_genes),
+        .data$Genes,
+        paste0("Many genes (", .data$`Gene count`, ")")
       ),
-      Transcripts = ifelse(many_genes == "few_genes" | is.na(many_genes), Transcripts, ""),
+      Transcripts = ifelse(.data$many_genes == "few_genes" | is.na(.data$many_genes), .data$Transcripts, ""),
     ) |>
     dplyr::select(-c("many_genes", "Gene count"))
 
@@ -278,18 +278,18 @@ set_many_transcripts_cnv <- function(x) {
   x.tmp <- x |>
     dplyr::rowwise() |>
     dplyr::mutate(
-      `Transcript count` = stringr::str_split(Transcripts, ", ") |> unlist() |> unique() |> length()
+      `Transcript count` = stringr::str_split(.data$Transcripts, ", ") |> unlist() |> unique() |> length()
     ) |>
     dplyr::ungroup() |>
     dplyr::mutate(
-      many_transcripts = ifelse(`Transcript count` > 2, "many_transcripts", "few_transcripts"),
+      many_transcripts = ifelse(.data$`Transcript count` > 2, "many_transcripts", "few_transcripts"),
     ) |>
     # Sort rows
-    dplyr::arrange(`Tier (top)`, `Event ID`)
+    dplyr::arrange(.data$`Tier (top)`, .data$`Event ID`)
 
   # Build the many transcripts table
   x.many_transcripts <- x.tmp |>
-    dplyr::filter(many_transcripts == "many_transcripts") |>
+    dplyr::filter(.data$many_transcripts == "many_transcripts") |>
     # Remove unneeded columns and rename others
     dplyr::select(
       "Event ID",
@@ -307,9 +307,9 @@ set_many_transcripts_cnv <- function(x) {
   x.ready <- x.tmp |>
     dplyr::mutate(
       Transcripts = ifelse(
-        many_transcripts == "few_transcripts" | is.na(many_transcripts),
-        Transcripts,
-        paste0("Many transcripts (", `Transcript count`, ")")
+        .data$many_transcripts == "few_transcripts" | is.na(.data$many_transcripts),
+        .data$Transcripts,
+        paste0("Many transcripts (", .data$`Transcript count`, ")")
       )
     ) |>
     dplyr::select(-c("many_transcripts", "Transcript count"))
@@ -383,14 +383,14 @@ process_cnv_tsv <- function(x) {
     # Reset sv_top_tier after removing annotations
     dplyr::group_by(`Event ID`) |>
     dplyr::mutate(
-      sv_top_tier = min(Tier),
-      "Tier (top)" = paste0(Tier, " (", sv_top_tier, ")"),
+      sv_top_tier = min(.data$Tier),
+      "Tier (top)" = paste0(.data$Tier, " (", .data$sv_top_tier, ")"),
     ) |>
     dplyr::ungroup() |>
     # Set unique annotation ID
     dplyr::mutate(`Annotation ID` = as.character(dplyr::row_number())) |>
     # Sort rows
-    dplyr::arrange(`Tier (top)`, `Event ID`)
+    dplyr::arrange(.data$`Tier (top)`, .data$`Event ID`)
 
   # Set column names
   column_selector <- c(
diff --git a/R/sv.R b/R/sv.R
index 9afdda8..a321919 100644
--- a/R/sv.R
+++ b/R/sv.R
@@ -165,12 +165,12 @@ split_svs <- function(x) {
 
   x.grouped <- x |>
     dplyr::group_by(
-      record_type = ifelse(Type %in% bps_types, "bps", "other")
+      record_type = ifelse(.data$Type %in% bps_types, "bps", "other")
     )
 
   keys <- x.grouped |>
     dplyr::group_keys() |>
-    dplyr::pull(record_type)
+    dplyr::pull("record_type")
 
   x.split <- x.grouped |>
     dplyr::group_split(.keep = FALSE) |>
@@ -211,12 +211,12 @@ remove_gene_fusion_dups <- function(.data, columns) {
   # Order elements of multi-entry effect values for reliable comparison
   v.groups <- c("frameshift_variant&gene_fusion", "gene_fusion")
   v.effects_ordered <- sapply(.data$Effect, function(s) {
-    c <- stringr::str_split(s, "&") |> unlist()
-    paste0(sort(c), collapse = "&")
+    c1 <- stringr::str_split(s, "&") |> unlist()
+    paste0(sort(c1), collapse = "&")
   })
 
   if (all(v.groups %in% v.effects_ordered)) {
-    .data |> dplyr::filter(Effect != "gene_fusion")
+    .data |> dplyr::filter(.data$Effect != "gene_fusion")
   } else {
     .data
   }
@@ -259,16 +259,16 @@ set_many_transcripts_sv <- function(x) {
   x.tmp <- x |>
     dplyr::rowwise() |>
     dplyr::mutate(
-      `Transcript count` = stringr::str_split(Transcripts, ", ") |> unlist() |> unique() |> length()
+      `Transcript count` = stringr::str_split(.data$Transcripts, ", ") |> unlist() |> unique() |> length()
     ) |>
     dplyr::ungroup() |>
     dplyr::mutate(
-      many_transcripts = ifelse(`Transcript count` > 2, "many_transcripts", "few_transcripts")
+      many_transcripts = ifelse(.data$`Transcript count` > 2, "many_transcripts", "few_transcripts")
     )
 
   # Build the many transcripts table
   mt <- x.tmp |>
-    dplyr::filter(many_transcripts == "many_transcripts") |>
+    dplyr::filter(.data$many_transcripts == "many_transcripts") |>
     # Remove unneeded columns and rename others
     dplyr::select(
       "Record ID",
@@ -284,12 +284,12 @@ set_many_transcripts_sv <- function(x) {
   x.ready <- x.tmp |>
     dplyr::mutate(
       Transcripts = ifelse(
-        many_transcripts == "few_transcripts" | is.na(many_transcripts),
-        Transcripts,
-        paste0("Many transcripts (", `Transcript count`, ")")
+        .data$many_transcripts == "few_transcripts" | is.na(.data$many_transcripts),
+        .data$Transcripts,
+        paste0("Many transcripts (", .data$`Transcript count`, ")")
       )
     ) |>
-    dplyr::select(-c(many_transcripts, `Transcript count`))
+    dplyr::select(-c("many_transcripts", "Transcript count"))
 
   list(
     many_transcripts = mt,
@@ -310,30 +310,30 @@ process_sv <- function(x) {
   # Prepare input
   sv.ready <- sv.input$data |>
     dplyr::mutate(
-      "annotation_count" = count_pieces(annotation, ","),
-      "Top Tier" = tier,
-      "SR_PR_ref" = paste0(SR_ref, ",", PR_ref),
+      "annotation_count" = count_pieces(.data$annotation, ","),
+      "Top Tier" = .data$tier,
+      "SR_PR_ref" = paste0(.data$SR_ref, ",", .data$PR_ref),
       "SR_PR_sum" = dplyr::case_when(
-        is.na(SR_alt) & is.na(PR_alt) ~ NA,
-        is.na(SR_alt) ~ PR_alt,
-        is.na(PR_alt) ~ SR_alt,
-        .default = SR_alt + PR_alt,
+        is.na(.data$SR_alt) & is.na(.data$PR_alt) ~ NA,
+        is.na(.data$SR_alt) ~ .data$PR_alt,
+        is.na(.data$PR_alt) ~ .data$SR_alt,
+        .default = .data$SR_alt + .data$PR_alt,
       ),
       "SR_PR_asm_sum" = dplyr::case_when(
-        is.na(SR_asm_alt) & is.na(PR_asm_alt) ~ NA,
-        is.na(SR_asm_alt) ~ PR_asm_alt,
-        is.na(PR_asm_alt) ~ SR_asm_alt,
-        .default = SR_asm_alt + PR_asm_alt,
+        is.na(.data$SR_asm_alt) & is.na(.data$PR_asm_alt) ~ NA,
+        is.na(.data$SR_asm_alt) ~ .data$PR_asm_alt,
+        is.na(.data$PR_asm_alt) ~ .data$SR_asm_alt,
+        .default = .data$SR_asm_alt + .data$PR_asm_alt,
       ),
-      start = paste(chrom, base::format(start, big.mark = ",", trim = TRUE), sep = ":"),
-      Type = ifelse(is.na(PURPLE_status), svtype, "PURPLE_inf"),
+      start = paste(.data$chrom, base::format(.data$start, big.mark = ",", trim = TRUE), sep = ":"),
+      Type = ifelse(is.na(.data$PURPLE_status), .data$svtype, "PURPLE_inf"),
       "Record ID" = dplyr::row_number(),
     ) |>
     dplyr::select(-c(
-      chrom,
-      PURPLE_status,
-      tier,
-      svtype,
+      "chrom",
+      "PURPLE_status",
+      "tier",
+      "svtype",
     ))
 
   # Split out breakpoints for merging
@@ -347,7 +347,7 @@ process_sv <- function(x) {
   cols_to_split <- c("AF_PURPLE", "CN_PURPLE")
   double_cols <- split_double_col(sv.tmp, cols_to_split)
   sv.tmp <- sv.tmp |>
-    dplyr::select(-c(cols_to_split)) |>
+    dplyr::select(-c("cols_to_split")) |>
     dplyr::bind_cols(double_cols)
 
   # Format a table for to be used as the SV Map
@@ -372,33 +372,33 @@ process_sv <- function(x) {
       "PURPLE AF" = "AF_PURPLE",
       "PURPLE CN" = "CN_PURPLE",
     ) |>
-    dplyr::arrange(`Record ID`)
+    dplyr::arrange(.data$`Record ID`)
 
   # Melt annotations
   sv.melted_all <- sv.tmp |>
     # Split into individual annotations
-    dplyr::mutate(annotation = strsplit(annotation, ",")) |>
+    dplyr::mutate(annotation = strsplit(.data$annotation, ",")) |>
     # Convert annotation fields into columns
-    tidyr::unnest(annotation) |>
+    tidyr::unnest(.data$annotation) |>
     tidyr::separate(
-      annotation, c("Event", "Effect", "Genes", "Transcripts", "Detail", "Tier"),
+      .data$annotation, c("Event", "Effect", "Genes", "Transcripts", "Detail", "Tier"),
       sep = "\\|", convert = FALSE
     ) |>
     # Remove gene_fusion annotations for variants where frameshift_variant&gene_fusion already exist
-    dplyr::group_by(across(-Effect)) |>
+    dplyr::group_by(dplyr::across(-.data$Effect)) |>
     dplyr::group_modify(remove_gene_fusion_dups) |>
     dplyr::ungroup() |>
     # Remove unused columns
-    dplyr::select(c(-Event, -ALT)) |>
+    dplyr::select(c(-.data$Event, -.data$ALT)) |>
     # Create columns, modify others
     dplyr::mutate(
       "Annotation ID" = dplyr::row_number(),
-      "Tier (top)" = paste0(Tier, " (", `Top Tier`, ")"),
-      "Genes" = stringr::str_replace_all(Genes, "&", ", "),
-      "Transcripts" = stringr::str_replace_all(Transcripts, "&", ", "),
+      "Tier (top)" = paste0(.data$Tier, " (", .data$`Top Tier`, ")"),
+      "Genes" = stringr::str_replace_all(.data$Genes, "&", ", "),
+      "Transcripts" = stringr::str_replace_all(.data$Transcripts, "&", ", "),
     ) |>
     # Sort rows
-    dplyr::arrange(`Tier (top)`, `Record ID`, Genes, Effect)
+    dplyr::arrange(.data$`Tier (top)`, .data$`Record ID`, .data$Genes, .data$Effect)
 
   # Abbreviate effects
   abbreviate_effectv <- Vectorize(abbreviate_effect)
diff --git a/R/umccrise.R b/R/umccrise.R
index 4a5b212..98ee386 100644
--- a/R/umccrise.R
+++ b/R/umccrise.R
@@ -30,7 +30,7 @@ bcftools_stats_plot <- function(x = NULL) {
   tot <- nrow(d)
   p <- d |>
     ggplot2::ggplot(ggplot2::aes(x = .data$qual)) +
-    ggplot2::geom_histogram(ggplot2::aes(y = ggplot2::after_stat(density)), binwidth = 4, fill = "lightblue") +
+    ggplot2::geom_histogram(ggplot2::aes(y = ggplot2::after_stat(stats::density)), binwidth = 4, fill = "lightblue") +
     ggplot2::geom_density(alpha = 0.6) +
     ggplot2::geom_vline(xintercept = med, colour = "blue", linetype = "dashed") +
     ggplot2::scale_x_continuous(n.breaks = 10) +
diff --git a/tests/testthat/test-roxytest-testexamples-purple.R b/tests/testthat/test-roxytest-testexamples-purple.R
index 46bdedc..81d1054 100644
--- a/tests/testthat/test-roxytest-testexamples-purple.R
+++ b/tests/testthat/test-roxytest-testexamples-purple.R
@@ -19,7 +19,7 @@ test_that("Function purple_cnv_som_gene_process() @ L60", {
 })
 
 
-test_that("Function purple_cnv_som_read() @ L447", {
+test_that("Function purple_cnv_som_read() @ L445", {
   
   x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
   (p <- purple_cnv_som_read(x))
@@ -27,7 +27,7 @@ test_that("Function purple_cnv_som_read() @ L447", {
 })
 
 
-test_that("Function purple_cnv_som_process() @ L480", {
+test_that("Function purple_cnv_som_process() @ L478", {
   
   x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
   (pp <- purple_cnv_som_process(x))
@@ -35,7 +35,7 @@ test_that("Function purple_cnv_som_process() @ L480", {
 })
 
 
-test_that("Function purple_qc_read() @ L548", {
+test_that("Function purple_qc_read() @ L546", {
   
   x <- system.file("extdata/purple/purple.qc", package = "gpgr")
   (q <- purple_qc_read(x))
@@ -43,7 +43,7 @@ test_that("Function purple_qc_read() @ L548", {
 })
 
 
-test_that("Function purple_purity_read() @ L606", {
+test_that("Function purple_purity_read() @ L604", {
   
   x <- system.file("extdata/purple/purple.purity.tsv", package = "gpgr")
   (p <- purple_purity_read(x))

From 12310d4dbc8ddde192f0cf504b004bd32330a836 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 6 May 2024 19:18:38 +1000
Subject: [PATCH 3/8] devtools check/styler - part3

---
 R/oncoviral.R                                 | 45 +++++++++----------
 R/purple.R                                    |  2 +-
 R/rmd.R                                       |  2 +
 man/cancer_rmd.Rd                             |  4 ++
 .../test-roxytest-testexamples-oncoviral.R    |  6 +--
 .../test-roxytest-testexamples-purple.R       |  2 +-
 6 files changed, 32 insertions(+), 29 deletions(-)

diff --git a/R/oncoviral.R b/R/oncoviral.R
index 7c87f0d..df33fc5 100644
--- a/R/oncoviral.R
+++ b/R/oncoviral.R
@@ -12,11 +12,10 @@
 #' x <- system.file("extdata/virusbreakend/virusbreakend.vcf.summary.tsv", package = "gpgr")
 #' (vb <- virusbreakend_summary_read(x))
 #' @testexamples
-#' expect_equal(colnames(vb)[ncol(vb)], "QCStatus")
+#' expect_equal(colnames(vb$tab)[ncol(vb$tab)], "QC")
 #'
 #' @export
 virusbreakend_summary_read <- function(x) {
-
   nm <- c(
     "taxid_genus" = "c",
     "name_genus" = "c",
@@ -44,7 +43,6 @@ virusbreakend_summary_read <- function(x) {
     "integrations" = "i",
     "QCStatus" = "c"
   )
-
   ctypes <- paste(nm, collapse = "")
   virusbreakend_summary <- readr::read_tsv(x, col_types = ctypes)
 
@@ -54,13 +52,13 @@ virusbreakend_summary_read <- function(x) {
 
     virusbreakend_summary <- virusbreakend_summary |>
       dplyr::select(
-        Virus="name_assigned",
-        Length="endpos",
-        Reads="numreads",
-        Coverage="coverage",
-        `Mean depth`="meandepth",
-        Intergrations="integrations",
-        QC="QCStatus",
+        Virus = "name_assigned",
+        Length = "endpos",
+        Reads = "numreads",
+        Coverage = "coverage",
+        `Mean depth` = "meandepth",
+        Intergrations = "integrations",
+        QC = "QCStatus",
       )
   }
 
@@ -71,7 +69,7 @@ virusbreakend_summary_read <- function(x) {
     "Reads", "Number of reads mapped to adjusted viral reference",
     "Coverage", "Percentage of viral positions with at least one read mapped",
     "Mean depth", "Mean alignment depth",
-    "Intergrations", "Number of detected integration breakpoints",
+    "Integrations", "Number of detected integration breakpoints",
     "QC", "QC status of viral intergrations",
   )
 
@@ -95,29 +93,28 @@ virusbreakend_summary_read <- function(x) {
 #' x <- system.file("extdata/virusbreakend/virusbreakend.vcf", package = "gpgr")
 #' (vb <- virusbreakend_vcf_read(x))
 #' @testexamples
-#' expect_equal(colnames(vb)[ncol(vb)], "QC")
+#' expect_equal(colnames(vb$tab)[ncol(vb$tab)], "QC")
 #'
 #' @export
 virusbreakend_vcf_read <- function(x) {
-
   d <- bedr::read.vcf(x, split.info = TRUE, verbose = FALSE)
 
   if (nrow(d$vcf) > 0) {
     virusbreakend_integrations <- tibble::as_tibble(d$vcf) |>
       dplyr::select(
-          Contig="CHROM",
-          Position="POS",
-          "Fragment support"="BVF",
-          "Fragment support (unmapped)"="BUM",
-          "Softclip read support"="BSC",
-          Reference="REF",
-          Alt="ALT",
-          `Breakend ID`="ID",
-          `Mate ID`="MATEID",
-          QC="FILTER",
+        Contig = "CHROM",
+        Position = "POS",
+        "Fragment support" = "BVF",
+        "Fragment support (unmapped)" = "BUM",
+        "Softclip read support" = "BSC",
+        Reference = "REF",
+        Alt = "ALT",
+        `Breakend ID` = "ID",
+        `Mate ID` = "MATEID",
+        QC = "FILTER",
       )
   } else {
-      virusbreakend_integrations <- tibble::tibble()
+    virusbreakend_integrations <- tibble::tibble()
   }
 
   descr <- dplyr::tribble(
diff --git a/R/purple.R b/R/purple.R
index 6a7fbbe..78f491f 100644
--- a/R/purple.R
+++ b/R/purple.R
@@ -12,7 +12,7 @@
 #' x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
 #' (p <- purple_cnv_som_gene_read(x))
 #' @testexamples
-#' expect_equal(colnames(p)[ncol(p)], "minMinorAlleleCopyNumber")
+#' expect_equal(colnames(p)[ncol(p)], "depthWindowCount")
 #'
 #' @export
 purple_cnv_som_gene_read <- function(x) {
diff --git a/R/rmd.R b/R/rmd.R
index 25a454c..6ca8f73 100644
--- a/R/rmd.R
+++ b/R/rmd.R
@@ -29,6 +29,8 @@
 #' @param tumor_name Name of tumor sample.
 #' @param out_file Path to output HTML file (needs '.html' suffix) (def: `{tumor_name}_cancer_report.html`).
 #' @param quiet Suppress log printing during rendering.
+#' @param bcftools_stats Path to `bcftools_stats.txt` file.
+#' @param dragen_hrd Path to DRAGEN `hrdscore.csv` file.
 #'
 #' @return Path to rendered HTML report.
 #' @export
diff --git a/man/cancer_rmd.Rd b/man/cancer_rmd.Rd
index e13b101..c361f4f 100644
--- a/man/cancer_rmd.Rd
+++ b/man/cancer_rmd.Rd
@@ -39,8 +39,12 @@ cancer_rmd(
 
 \item{batch_name}{Name of batch sample.}
 
+\item{bcftools_stats}{Path to \code{bcftools_stats.txt} file.}
+
 \item{conda_list}{Path to \code{conda_pkg_list.txt} file.}
 
+\item{dragen_hrd}{Path to DRAGEN \code{hrdscore.csv} file.}
+
 \item{img_dir}{Path to directory containing PURPLE plots.}
 
 \item{key_genes}{Path to UMCCR cancer gene file.}
diff --git a/tests/testthat/test-roxytest-testexamples-oncoviral.R b/tests/testthat/test-roxytest-testexamples-oncoviral.R
index cad645a..a1c116d 100644
--- a/tests/testthat/test-roxytest-testexamples-oncoviral.R
+++ b/tests/testthat/test-roxytest-testexamples-oncoviral.R
@@ -6,14 +6,14 @@ test_that("Function virusbreakend_summary_read() @ L18", {
   
   x <- system.file("extdata/virusbreakend/virusbreakend.vcf.summary.tsv", package = "gpgr")
   (vb <- virusbreakend_summary_read(x))
-  expect_equal(colnames(vb)[ncol(vb)], "QCStatus")
+  expect_equal(colnames(vb$tab)[ncol(vb$tab)], "QC")
 })
 
 
-test_that("Function virusbreakend_vcf_read() @ L101", {
+test_that("Function virusbreakend_vcf_read() @ L99", {
   
   x <- system.file("extdata/virusbreakend/virusbreakend.vcf", package = "gpgr")
   (vb <- virusbreakend_vcf_read(x))
-  expect_equal(colnames(vb)[ncol(vb)], "QC")
+  expect_equal(colnames(vb$tab)[ncol(vb$tab)], "QC")
 })
 
diff --git a/tests/testthat/test-roxytest-testexamples-purple.R b/tests/testthat/test-roxytest-testexamples-purple.R
index 81d1054..19d2926 100644
--- a/tests/testthat/test-roxytest-testexamples-purple.R
+++ b/tests/testthat/test-roxytest-testexamples-purple.R
@@ -6,7 +6,7 @@ test_that("Function purple_cnv_som_gene_read() @ L18", {
   
   x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
   (p <- purple_cnv_som_gene_read(x))
-  expect_equal(colnames(p)[ncol(p)], "minMinorAlleleCopyNumber")
+  expect_equal(colnames(p)[ncol(p)], "depthWindowCount")
 })
 
 

From bd1715a848a9700635cd90a3f62191ed9a72339e Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 6 May 2024 22:19:00 +1000
Subject: [PATCH 4/8] devnotes: replace pcgr reference

---
 vignettes/devnotes.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/devnotes.Rmd b/vignettes/devnotes.Rmd
index a43ef8a..808f998 100644
--- a/vignettes/devnotes.Rmd
+++ b/vignettes/devnotes.Rmd
@@ -18,7 +18,7 @@ then work with `devtools`. You'll also need to install
 | `devtools::load_all()` | load the pkg (`Cmd+Shift+L`) |
 | `devtools::check()` | check the pkg (`Cmd+Shift+E`) |
 | `devtools::install()` | install the pkg (`Cmd+Shift+B`) |
-| `R CMD INSTALL --no-multiarch --with-keep.source pcgr.git/pcgrr` | install the pkg into the first library of `.libPaths()` (useful when using in conda env) |
+| `R CMD INSTALL --no-multiarch --with-keep.source git/gpgr` | install the pkg into the first library of `.libPaths()` (useful when using in conda env) |
 
 ### Data Version Control
 

From 39b3cdf32daff1d0ae06be436b2a286eca840e1d Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 6 May 2024 23:45:16 +1000
Subject: [PATCH 5/8] use v24.03.0 umccr cancer gene panel

---
 R/purple.R                                    | 21 ++++++------
 data-raw/umccr_cancer_genes.R                 | 33 ++++++++-----------
 man/purple_cnv_som_gene_process.Rd            |  8 ++---
 .../test-roxytest-testexamples-purple.R       | 10 +++---
 4 files changed, 32 insertions(+), 40 deletions(-)

diff --git a/R/purple.R b/R/purple.R
index 78f491f..2cc74f4 100644
--- a/R/purple.R
+++ b/R/purple.R
@@ -36,12 +36,12 @@ purple_cnv_som_gene_read <- function(x) {
 #' Process PURPLE CNV Gene File for UMCCRISE
 #'
 #' Processes the `purple.cnv.gene.tsv` file. Keeps genes that are in the
-#' [UMCCR cancer gene list](https://github.com/umccr/genes/blob/893a655801ce92715f05517b5052e4e81904e870/panels/umccr_2019-03-20.tsv)
-#' and selects columns of interest.
+#' UMCCR cancer gene list
+#' ([v24.03.0](https://raw.githubusercontent.com/umccr/gene_panels/v24.03.0/somatic_panel/3_final_panel/final_panel.tsv)) and selects columns of interest.
 #'
 #' @param x Path to `purple.cnv.gene.tsv` file.
 #' @param g Path to gene file containing at least three columns:
-#' * `ensembl_gene_symbol`: gene name (character).
+#' * `symbol`: gene name (character).
 #' * `tsgene`: is this gene a tumor suppressor (TRUE/FALSE).
 #' * `oncogene`: is this gene an oncogene (TRUE/FALSE).
 #'
@@ -51,7 +51,7 @@ purple_cnv_som_gene_read <- function(x) {
 #'
 #' @examples
 #' x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
-#' g <- system.file("extdata/ref/umccr_cancer_genes_2019-03-20.tsv", package = "gpgr")
+#' g <- system.file("extdata/ref/umccr_cancer_genes_v24.03.0.tsv", package = "gpgr")
 #' (pp <- purple_cnv_som_gene_process(x, g))
 #' @testexamples
 #' expect_equal(colnames(pp$tab)[ncol(pp$tab)], "minRegSupportStartEndMethod")
@@ -60,22 +60,21 @@ purple_cnv_som_gene_read <- function(x) {
 purple_cnv_som_gene_process <- function(x, g = NULL) {
   purple_cnv_gene <- purple_cnv_som_gene_read(x)
   if (is.null(g)) {
-    g <- system.file("extdata/ref/umccr_cancer_genes_2019-03-20.tsv", package = "gpgr")
+    g <- system.file("extdata/ref/umccr_cancer_genes_v24.03.0.tsv", package = "gpgr")
   }
   genes <-
     readr::read_tsv(g, col_types = readr::cols(
-      ensembl_gene_symbol = "c", oncogene = "l", tsgene = "l"
+      symbol = "c", oncogene = "l", tumorsuppressor = "l"
     )) |>
-    dplyr::select("ensembl_gene_symbol", "oncogene", "tsgene")
+    dplyr::select("symbol", "oncogene", tsgene = "tumorsuppressor")
   oncogenes <- genes |>
     dplyr::filter(.data$oncogene) |>
-    dplyr::pull(.data$ensembl_gene_symbol)
+    dplyr::pull(.data$symbol)
   tsgenes <- genes |>
     dplyr::filter(.data$tsgene) |>
-    dplyr::pull(.data$ensembl_gene_symbol)
-
+    dplyr::pull(.data$symbol)
   purple_cnv_gene <- purple_cnv_gene |>
-    dplyr::filter(.data$gene %in% genes$ensembl_gene_symbol) |>
+    dplyr::filter(.data$gene %in% genes$symbol) |>
     dplyr::mutate(
       chromosome = as.factor(.data$chromosome),
       transcriptID = paste0(.data$transcriptId),
diff --git a/data-raw/umccr_cancer_genes.R b/data-raw/umccr_cancer_genes.R
index 2da79d6..636cfa9 100644
--- a/data-raw/umccr_cancer_genes.R
+++ b/data-raw/umccr_cancer_genes.R
@@ -1,23 +1,16 @@
 # UMCCR Cancer Genes
-require(here)
-require(readr)
+require(here, include.only = "here")
+require(readr, include.only = "read_tsv")
 require(dplyr)
+require(glue, include.only = "glue")
 
-tmp <- tempfile()
-download.file(
-  url = "https://raw.githubusercontent.com/umccr/genes/893a655801ce92715f05517b5052e4e81904e870/panels/umccr_2019-03-20.tsv",
-  destfile = tmp
-)
-
-readr::read_tsv(tmp) |>
-  dplyr::select(symbol, tumorsuppressor, oncogene) |>
-  readr::write_tsv(here("inst/extdata/ref/umccr_cancer_genes_2019-03-20.tsv"))
-
-tmp2 <- tempfile()
-download.file(
-  "https://raw.githubusercontent.com/umccr/workflows/8d06a16a0199ccf94b666f9ec027efce8af1110b/genes/cancer_genes/umccr_cancer_genes.hg38.coding.bed",
-  destfile = tmp2
-)
-
-readr::read_tsv(tmp2, col_names = c("chr", "start", "end", "symbol"), col_types = "ciic") |>
-  readr::write_tsv(here("inst/extdata/ref/umccr_cancer_genes_hg38_coding.bed"))
+version <- "24.03.0"
+read_umccr_genes_final_panel <- function(version) {
+  repo <- "https://raw.githubusercontent.com/umccr/gene_panels"
+  tsv_url <- glue::glue("{repo}/v{version}/somatic_panel/3_final_panel/final_panel.tsv")
+  d <- readr::read_tsv(tsv_url, col_types = readr::cols(.default = "c", "tsgene" = "l", "oncogene" = "l")) |>
+    dplyr::select(symbol = "hgnc_symbol", tumorsuppressor = "tsgene", "oncogene")
+  d
+}
+read_umccr_genes_final_panel(version) |>
+  readr::write_tsv(here(glue("inst/extdata/ref/umccr_cancer_genes_v{version}.tsv")))
diff --git a/man/purple_cnv_som_gene_process.Rd b/man/purple_cnv_som_gene_process.Rd
index a859cad..853cb94 100644
--- a/man/purple_cnv_som_gene_process.Rd
+++ b/man/purple_cnv_som_gene_process.Rd
@@ -11,7 +11,7 @@ purple_cnv_som_gene_process(x, g = NULL)
 
 \item{g}{Path to gene file containing at least three columns:
 \itemize{
-\item \code{ensembl_gene_symbol}: gene name (character).
+\item \code{symbol}: gene name (character).
 \item \code{tsgene}: is this gene a tumor suppressor (TRUE/FALSE).
 \item \code{oncogene}: is this gene an oncogene (TRUE/FALSE).
 }}
@@ -25,11 +25,11 @@ List with two elements:
 }
 \description{
 Processes the \code{purple.cnv.gene.tsv} file. Keeps genes that are in the
-\href{https://github.com/umccr/genes/blob/893a655801ce92715f05517b5052e4e81904e870/panels/umccr_2019-03-20.tsv}{UMCCR cancer gene list}
-and selects columns of interest.
+UMCCR cancer gene list
+(\href{https://raw.githubusercontent.com/umccr/gene_panels/v24.03.0/somatic_panel/3_final_panel/final_panel.tsv}{v24.03.0}) and selects columns of interest.
 }
 \examples{
 x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
-g <- system.file("extdata/ref/umccr_cancer_genes_2019-03-20.tsv", package = "gpgr")
+g <- system.file("extdata/ref/umccr_cancer_genes_v24.03.0.tsv", package = "gpgr")
 (pp <- purple_cnv_som_gene_process(x, g))
 }
diff --git a/tests/testthat/test-roxytest-testexamples-purple.R b/tests/testthat/test-roxytest-testexamples-purple.R
index 19d2926..eac038f 100644
--- a/tests/testthat/test-roxytest-testexamples-purple.R
+++ b/tests/testthat/test-roxytest-testexamples-purple.R
@@ -13,13 +13,13 @@ test_that("Function purple_cnv_som_gene_read() @ L18", {
 test_that("Function purple_cnv_som_gene_process() @ L60", {
   
   x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
-  g <- system.file("extdata/ref/umccr_cancer_genes_2019-03-20.tsv", package = "gpgr")
+  g <- system.file("extdata/ref/umccr_cancer_genes_v24.03.0.tsv", package = "gpgr")
   (pp <- purple_cnv_som_gene_process(x, g))
   expect_equal(colnames(pp$tab)[ncol(pp$tab)], "minRegSupportStartEndMethod")
 })
 
 
-test_that("Function purple_cnv_som_read() @ L445", {
+test_that("Function purple_cnv_som_read() @ L444", {
   
   x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
   (p <- purple_cnv_som_read(x))
@@ -27,7 +27,7 @@ test_that("Function purple_cnv_som_read() @ L445", {
 })
 
 
-test_that("Function purple_cnv_som_process() @ L478", {
+test_that("Function purple_cnv_som_process() @ L477", {
   
   x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
   (pp <- purple_cnv_som_process(x))
@@ -35,7 +35,7 @@ test_that("Function purple_cnv_som_process() @ L478", {
 })
 
 
-test_that("Function purple_qc_read() @ L546", {
+test_that("Function purple_qc_read() @ L545", {
   
   x <- system.file("extdata/purple/purple.qc", package = "gpgr")
   (q <- purple_qc_read(x))
@@ -43,7 +43,7 @@ test_that("Function purple_qc_read() @ L546", {
 })
 
 
-test_that("Function purple_purity_read() @ L604", {
+test_that("Function purple_purity_read() @ L603", {
   
   x <- system.file("extdata/purple/purple.purity.tsv", package = "gpgr")
   (p <- purple_purity_read(x))

From 00c8b2eb68c276287a1b4a46b8e0ce0bee73c1ef Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Tue, 7 May 2024 00:16:14 +1000
Subject: [PATCH 6/8] devtools check/styler - part4

---
 R/oncokb.R                                         |  5 +++++
 R/purple.R                                         | 11 +++++++----
 R/sv.R                                             |  2 ++
 tests/testthat/test-roxytest-testexamples-purple.R |  4 ++--
 4 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/R/oncokb.R b/R/oncokb.R
index 8f3963f..f506629 100644
--- a/R/oncokb.R
+++ b/R/oncokb.R
@@ -1,3 +1,5 @@
+#' @param x Path to something.
+#'
 #' @export
 read_oncokb <- function(x) {
   readr::read_tsv(x) |>
@@ -7,6 +9,9 @@ read_oncokb <- function(x) {
     dplyr::pull("Hugo Symbol")
 }
 
+#' @param x Path to something.
+#' @param oncokb_genes Tibble of something.
+#'
 #' @export
 get_oncokb_genes <- function(x, oncokb_genes) {
   delimiters <- " ,&-"
diff --git a/R/purple.R b/R/purple.R
index 2cc74f4..08f33b7 100644
--- a/R/purple.R
+++ b/R/purple.R
@@ -319,6 +319,8 @@ set_many_transcripts_cnv <- function(x) {
   )
 }
 
+#' @param x Path to something.
+#'
 #' @export
 process_cnv_tsv <- function(x) {
   # Read input
@@ -539,7 +541,7 @@ purple_cnv_som_process <- function(x) {
 #' x <- system.file("extdata/purple/purple.qc", package = "gpgr")
 #' (q <- purple_qc_read(x))
 #' @testexamples
-#' expect_true(q$raw[1, "value", drop = TRUE] == "WARN_DELETED_GENES")
+#' expect_true(q$raw[1, "value", drop = TRUE] == "FAIL_CONTAMINATION")
 #'
 #' @export
 purple_qc_read <- function(x) {
@@ -551,7 +553,7 @@ purple_qc_read <- function(x) {
     "QCStatus", "Method", "CopyNumberSegments",
     "UnsupportedCopyNumberSegments", "Purity", "AmberGender",
     "CobaltGender", "DeletedGenes", "Contamination", "GermlineAberrations",
-    "AmberMeanDepth", "LohPercent"
+    "AmberMeanDepth"
   )
 
   assertthat::assert_that(all(purple_qc$key == nm))
@@ -597,7 +599,7 @@ purple_qc_read <- function(x) {
 #' (p <- purple_purity_read(x))
 #' @testexamples
 #' expect_equal(p$raw[1, "column", drop = TRUE], "purity")
-#' expect_equal(p$raw[nrow(p$raw), "column", drop = TRUE], "svTumorMutationalBurden")
+#' expect_equal(p$raw[nrow(p$raw), "column", drop = TRUE], "targeted")
 #'
 #' @export
 purple_purity_read <- function(x) {
@@ -617,6 +619,7 @@ purple_purity_read <- function(x) {
     "maxPloidy", "d",
     "minDiploidProportion", "d",
     "maxDiploidProportion", "d",
+    "version", "c",
     "somaticPenalty", "d",
     "wholeGenomeDuplication", "c",
     "msIndelsPerMb", "d",
@@ -637,7 +640,7 @@ purple_purity_read <- function(x) {
 
   purple_purity <- purple_purity |>
     dplyr::mutate(
-      dplyr::across(tidyselect::vars_select_helpers$where(is.numeric), round, 2),
+      dplyr::across(tidyselect::where(is.numeric), \(x) round(x, 2)),
       dplyr::across(dplyr::everything(), as.character)
     ) |>
     tidyr::pivot_longer(dplyr::everything(), names_to = "column", values_to = "value") |>
diff --git a/R/sv.R b/R/sv.R
index a321919..0c4adad 100644
--- a/R/sv.R
+++ b/R/sv.R
@@ -297,6 +297,8 @@ set_many_transcripts_sv <- function(x) {
   )
 }
 
+#' @param x Path to something.
+#'
 #' @export
 process_sv <- function(x) {
   # Read input and set column information
diff --git a/tests/testthat/test-roxytest-testexamples-purple.R b/tests/testthat/test-roxytest-testexamples-purple.R
index eac038f..3f83ec0 100644
--- a/tests/testthat/test-roxytest-testexamples-purple.R
+++ b/tests/testthat/test-roxytest-testexamples-purple.R
@@ -39,7 +39,7 @@ test_that("Function purple_qc_read() @ L545", {
   
   x <- system.file("extdata/purple/purple.qc", package = "gpgr")
   (q <- purple_qc_read(x))
-  expect_true(q$raw[1, "value", drop = TRUE] == "WARN_DELETED_GENES")
+  expect_true(q$raw[1, "value", drop = TRUE] == "FAIL_CONTAMINATION")
 })
 
 
@@ -48,6 +48,6 @@ test_that("Function purple_purity_read() @ L603", {
   x <- system.file("extdata/purple/purple.purity.tsv", package = "gpgr")
   (p <- purple_purity_read(x))
   expect_equal(p$raw[1, "column", drop = TRUE], "purity")
-  expect_equal(p$raw[nrow(p$raw), "column", drop = TRUE], "svTumorMutationalBurden")
+  expect_equal(p$raw[nrow(p$raw), "column", drop = TRUE], "targeted")
 })
 

From bb85163450e0134ee903a0f8afd0da6af71815d5 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Tue, 7 May 2024 01:31:26 +1000
Subject: [PATCH 7/8] devtools check/styler - part5

---
 R/oncokb.R                                    |  8 ++++-
 R/purple.R                                    | 33 +++++++++--------
 R/rmd.R                                       |  4 +--
 R/sv.R                                        | 35 ++++++++++---------
 man/cancer_rmd.Rd                             |  4 +--
 man/get_oncokb_genes.Rd                       | 19 ++++++++++
 man/plot_bnd_sr_pr_tot_hist.Rd                |  4 +--
 man/plot_bnd_sr_pr_tot_lines.Rd               |  4 +--
 man/process_cnv_tsv.Rd                        | 17 +++++++++
 man/process_sv.Rd                             | 17 +++++++++
 man/read_oncokb.Rd                            | 17 +++++++++
 .../test-roxytest-testexamples-purple.R       |  8 ++---
 12 files changed, 126 insertions(+), 44 deletions(-)
 create mode 100644 man/get_oncokb_genes.Rd
 create mode 100644 man/process_cnv_tsv.Rd
 create mode 100644 man/process_sv.Rd
 create mode 100644 man/read_oncokb.Rd

diff --git a/R/oncokb.R b/R/oncokb.R
index f506629..de557ef 100644
--- a/R/oncokb.R
+++ b/R/oncokb.R
@@ -1,5 +1,8 @@
+#' Read OncoKB
+#'
 #' @param x Path to something.
 #'
+#' @return Vector of genes.
 #' @export
 read_oncokb <- function(x) {
   readr::read_tsv(x) |>
@@ -9,8 +12,11 @@ read_oncokb <- function(x) {
     dplyr::pull("Hugo Symbol")
 }
 
+#' Get OncoKB Genes From Somewhere
+#'
 #' @param x Path to something.
-#' @param oncokb_genes Tibble of something.
+#' @param oncokb_genes A tibble of something.
+#' @return A vector I think.
 #'
 #' @export
 get_oncokb_genes <- function(x, oncokb_genes) {
diff --git a/R/purple.R b/R/purple.R
index 08f33b7..1046aa4 100644
--- a/R/purple.R
+++ b/R/purple.R
@@ -319,8 +319,12 @@ set_many_transcripts_cnv <- function(x) {
   )
 }
 
+#' Process CNV TSV
+#'
 #' @param x Path to something.
 #'
+#' @return List of many things.
+#'
 #' @export
 process_cnv_tsv <- function(x) {
   # Read input
@@ -342,19 +346,18 @@ process_cnv_tsv <- function(x) {
     dplyr::mutate(annotation = strsplit(.data$simple_ann, ",")) |>
     # Convert annotation fields into columns
     tidyr::unnest("annotation") |>
-    tidyr::separate(
-      "annotation",
-      c("Event", "Effect", "Genes", "Transcripts", "Detail", "Tier"),
-      sep = "\\|", convert = FALSE
+    tidyr::separate_wider_delim(
+      cols = "annotation", delim = "|",
+      names = c("Event", "Effect", "Genes", "Transcripts", "Detail", "Tier")
     ) |>
     # Create new columns and modify existing ones
     dplyr::mutate(
-      copyNumber = as.numeric(.data$copyNumber) |> round(2) %>% sprintf("%.2f", .),
-      minorAlleleCopyNumber = as.numeric(minorAlleleCopyNumber) |> round(2) %>% sprintf("%.2f", .),
-      majorAlleleCopyNumber = as.numeric(majorAlleleCopyNumber) |> round(2) %>% sprintf("%.2f", .),
-      "PURPLE CN Min+Maj" = paste0(minorAlleleCopyNumber, "+", majorAlleleCopyNumber),
-      "Genes" = stringr::str_replace_all(Genes, "&", ", "),
-      "Transcripts" = stringr::str_replace_all(Transcripts, "&", ", "),
+      copyNumber = sprintf("%.2f", round(as.numeric(.data$copyNumber), 2)),
+      minorAlleleCopyNumber = sprintf("%.2f", round(as.numeric(.data$minorAlleleCopyNumber), 2)),
+      majorAlleleCopyNumber = sprintf("%.2f", round(as.numeric(.data$majorAlleleCopyNumber), 2)),
+      "PURPLE CN Min+Maj" = paste0(.data$minorAlleleCopyNumber, "+", .data$majorAlleleCopyNumber),
+      "Genes" = stringr::str_replace_all(.data$Genes, "&", ", "),
+      "Transcripts" = stringr::str_replace_all(.data$Transcripts, "&", ", ")
     ) |>
     # Remove unused columns
     dplyr::select(-c(
@@ -369,7 +372,7 @@ process_cnv_tsv <- function(x) {
       "segmentEndSupport",
       "segmentStartSupport",
       "sv_top_tier",
-      "simple_ann",
+      "simple_ann"
     ))
 
   # Abbreviate effects
@@ -382,10 +385,10 @@ process_cnv_tsv <- function(x) {
   # Complete processing
   cnv.tmp <- cnv.annotations.split$retained |>
     # Reset sv_top_tier after removing annotations
-    dplyr::group_by(`Event ID`) |>
+    dplyr::group_by(.data$`Event ID`) |>
     dplyr::mutate(
       sv_top_tier = min(.data$Tier),
-      "Tier (top)" = paste0(.data$Tier, " (", .data$sv_top_tier, ")"),
+      "Tier (top)" = paste0(.data$Tier, " (", .data$sv_top_tier, ")")
     ) |>
     dplyr::ungroup() |>
     # Set unique annotation ID
@@ -408,8 +411,8 @@ process_cnv_tsv <- function(x) {
     "PURPLE CN" = "copyNumber",
     "PURPLE CN Min+Maj"
   )
-  cnv.tmp <- dplyr::select("cnv.tmp", tidyselect::all_of(c(column_selector, "Tier")))
-  cnv.filtered <- dplyr::select(cnv.annotations.split$filtered, tidyselect::any_of(column_selector))
+  cnv.tmp <- dplyr::select(cnv.tmp, dplyr::all_of(c(column_selector, "Tier")))
+  cnv.filtered <- dplyr::select(cnv.annotations.split$filtered, dplyr::any_of(column_selector))
 
   # Collapse selected annotations and set many genes
   cnv.many_genes_data <- set_many_genes_cnv(cnv.tmp)
diff --git a/R/rmd.R b/R/rmd.R
index 6ca8f73..dde3d6e 100644
--- a/R/rmd.R
+++ b/R/rmd.R
@@ -24,8 +24,8 @@
 #' @param result_outdir Path to directory to write tidy JSON/TSV results.
 #' @param somatic_snv_vcf Path to `somatic-PASS.vcf.gz` SNV VCF.
 #' @param somatic_snv_summary Path to `somatic_snv_summary.json` JSON.
-#' @param somatic_sv_tsv Path to `manta.tsv` TSV file.
-#' @param somatic_sv_vcf Path to `manta.vcf.gz` VCF file.
+#' @param somatic_sv_tsv Path to SV TSV file.
+#' @param somatic_sv_vcf Path to SV VCF file.
 #' @param tumor_name Name of tumor sample.
 #' @param out_file Path to output HTML file (needs '.html' suffix) (def: `{tumor_name}_cancer_report.html`).
 #' @param quiet Suppress log printing during rendering.
diff --git a/R/sv.R b/R/sv.R
index 0c4adad..6a4ede5 100644
--- a/R/sv.R
+++ b/R/sv.R
@@ -297,7 +297,10 @@ set_many_transcripts_sv <- function(x) {
   )
 }
 
-#' @param x Path to something.
+#' Process SV TSV
+#'
+#' @param x Path to SV TSV.
+#' @return List of many things.
 #'
 #' @export
 process_sv <- function(x) {
@@ -329,13 +332,13 @@ process_sv <- function(x) {
       ),
       start = paste(.data$chrom, base::format(.data$start, big.mark = ",", trim = TRUE), sep = ":"),
       Type = ifelse(is.na(.data$PURPLE_status), .data$svtype, "PURPLE_inf"),
-      "Record ID" = dplyr::row_number(),
+      "Record ID" = dplyr::row_number()
     ) |>
     dplyr::select(-c(
       "chrom",
       "PURPLE_status",
       "tier",
-      "svtype",
+      "svtype"
     ))
 
   # Split out breakpoints for merging
@@ -349,7 +352,7 @@ process_sv <- function(x) {
   cols_to_split <- c("AF_PURPLE", "CN_PURPLE")
   double_cols <- split_double_col(sv.tmp, cols_to_split)
   sv.tmp <- sv.tmp |>
-    dplyr::select(-c("cols_to_split")) |>
+    dplyr::select(-c(dplyr::all_of(cols_to_split))) |>
     dplyr::bind_cols(double_cols)
 
   # Format a table for to be used as the SV Map
@@ -372,7 +375,7 @@ process_sv <- function(x) {
       "IC_alt",
       "SR_PR_ref",
       "PURPLE AF" = "AF_PURPLE",
-      "PURPLE CN" = "CN_PURPLE",
+      "PURPLE CN" = "CN_PURPLE"
     ) |>
     dplyr::arrange(.data$`Record ID`)
 
@@ -381,17 +384,17 @@ process_sv <- function(x) {
     # Split into individual annotations
     dplyr::mutate(annotation = strsplit(.data$annotation, ",")) |>
     # Convert annotation fields into columns
-    tidyr::unnest(.data$annotation) |>
-    tidyr::separate(
-      .data$annotation, c("Event", "Effect", "Genes", "Transcripts", "Detail", "Tier"),
-      sep = "\\|", convert = FALSE
+    tidyr::unnest("annotation") |>
+    tidyr::separate_wider_delim(
+      cols = "annotation", delim = "|",
+      names = c("Event", "Effect", "Genes", "Transcripts", "Detail", "Tier")
     ) |>
     # Remove gene_fusion annotations for variants where frameshift_variant&gene_fusion already exist
-    dplyr::group_by(dplyr::across(-.data$Effect)) |>
+    dplyr::group_by(dplyr::across(-"Effect")) |>
     dplyr::group_modify(remove_gene_fusion_dups) |>
     dplyr::ungroup() |>
     # Remove unused columns
-    dplyr::select(c(-.data$Event, -.data$ALT)) |>
+    dplyr::select(-c("Event", "ALT")) |>
     # Create columns, modify others
     dplyr::mutate(
       "Annotation ID" = dplyr::row_number(),
@@ -432,7 +435,7 @@ process_sv <- function(x) {
       "PURPLE CN" = "CN_PURPLE",
       # Dropped after ops for non-map outputs
       "Top Tier",
-      "Type",
+      "Type"
     )
 
   # Create and set many transcript values
@@ -464,8 +467,8 @@ process_sv <- function(x) {
 #' @return A ggplot2 plot object.
 #'
 #' @examples
-#' x <- system.file("extdata/umccrise/sv/manta.tsv", package = "gpgr")
-#' d <- process_sv(x)$unmelted
+#' x <- system.file("extdata/sash/sv.prioritised.tsv", package = "gpgr")
+#' d <- process_sv(x)$map
 #' plot_bnd_sr_pr_tot_lines(d)
 #' @export
 plot_bnd_sr_pr_tot_lines <- function(d,
@@ -527,8 +530,8 @@ plot_bnd_sr_pr_tot_lines <- function(d,
 #' @return A ggplot2 plot object.
 #'
 #' @examples
-#' x <- system.file("extdata/umccrise/sv/manta.tsv", package = "gpgr")
-#' d <- process_sv(x)$unmelted
+#' x <- system.file("extdata/sash/sv.prioritised.tsv", package = "gpgr")
+#' d <- process_sv(x)$map
 #' plot_bnd_sr_pr_tot_hist(d, "a title")
 #' @export
 plot_bnd_sr_pr_tot_hist <- function(d,
diff --git a/man/cancer_rmd.Rd b/man/cancer_rmd.Rd
index c361f4f..8845848 100644
--- a/man/cancer_rmd.Rd
+++ b/man/cancer_rmd.Rd
@@ -71,9 +71,9 @@ cancer_rmd(
 
 \item{somatic_snv_summary}{Path to \code{somatic_snv_summary.json} JSON.}
 
-\item{somatic_sv_tsv}{Path to \code{manta.tsv} TSV file.}
+\item{somatic_sv_tsv}{Path to SV TSV file.}
 
-\item{somatic_sv_vcf}{Path to \code{manta.vcf.gz} VCF file.}
+\item{somatic_sv_vcf}{Path to SV VCF file.}
 
 \item{result_outdir}{Path to directory to write tidy JSON/TSV results.}
 
diff --git a/man/get_oncokb_genes.Rd b/man/get_oncokb_genes.Rd
new file mode 100644
index 0000000..21bd062
--- /dev/null
+++ b/man/get_oncokb_genes.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/oncokb.R
+\name{get_oncokb_genes}
+\alias{get_oncokb_genes}
+\title{Get OncoKB Genes From Somewhere}
+\usage{
+get_oncokb_genes(x, oncokb_genes)
+}
+\arguments{
+\item{x}{Path to something.}
+
+\item{oncokb_genes}{A tibble of something.}
+}
+\value{
+A vector I think.
+}
+\description{
+Get OncoKB Genes From Somewhere
+}
diff --git a/man/plot_bnd_sr_pr_tot_hist.Rd b/man/plot_bnd_sr_pr_tot_hist.Rd
index c060067..19538fd 100644
--- a/man/plot_bnd_sr_pr_tot_hist.Rd
+++ b/man/plot_bnd_sr_pr_tot_hist.Rd
@@ -25,7 +25,7 @@ Plots histograms for the number of split reads (\code{SR}), paired end reads (\c
 sum (\code{tot}) across all BNDs. Observations where the SR or PR value is 0 (NA) are not shown.
 }
 \examples{
-x <- system.file("extdata/umccrise/sv/manta.tsv", package = "gpgr")
-d <- process_sv(x)$unmelted
+x <- system.file("extdata/sash/sv.prioritised.tsv", package = "gpgr")
+d <- process_sv(x)$map
 plot_bnd_sr_pr_tot_hist(d, "a title")
 }
diff --git a/man/plot_bnd_sr_pr_tot_lines.Rd b/man/plot_bnd_sr_pr_tot_lines.Rd
index 82e8e51..b0cae9d 100644
--- a/man/plot_bnd_sr_pr_tot_lines.Rd
+++ b/man/plot_bnd_sr_pr_tot_lines.Rd
@@ -25,7 +25,7 @@ Plots the number of split reads (\code{SR}), paired end reads (\code{PR}), and t
 sum (\code{tot}) across all BNDs, sorted by \code{tot}.
 }
 \examples{
-x <- system.file("extdata/umccrise/sv/manta.tsv", package = "gpgr")
-d <- process_sv(x)$unmelted
+x <- system.file("extdata/sash/sv.prioritised.tsv", package = "gpgr")
+d <- process_sv(x)$map
 plot_bnd_sr_pr_tot_lines(d)
 }
diff --git a/man/process_cnv_tsv.Rd b/man/process_cnv_tsv.Rd
new file mode 100644
index 0000000..1b5d772
--- /dev/null
+++ b/man/process_cnv_tsv.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/purple.R
+\name{process_cnv_tsv}
+\alias{process_cnv_tsv}
+\title{Process CNV TSV}
+\usage{
+process_cnv_tsv(x)
+}
+\arguments{
+\item{x}{Path to something.}
+}
+\value{
+List of many things.
+}
+\description{
+Process CNV TSV
+}
diff --git a/man/process_sv.Rd b/man/process_sv.Rd
new file mode 100644
index 0000000..38986b5
--- /dev/null
+++ b/man/process_sv.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sv.R
+\name{process_sv}
+\alias{process_sv}
+\title{Process SV TSV}
+\usage{
+process_sv(x)
+}
+\arguments{
+\item{x}{Path to SV TSV.}
+}
+\value{
+List of many things.
+}
+\description{
+Process SV TSV
+}
diff --git a/man/read_oncokb.Rd b/man/read_oncokb.Rd
new file mode 100644
index 0000000..43313e0
--- /dev/null
+++ b/man/read_oncokb.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/oncokb.R
+\name{read_oncokb}
+\alias{read_oncokb}
+\title{Read OncoKB}
+\usage{
+read_oncokb(x)
+}
+\arguments{
+\item{x}{Path to something.}
+}
+\value{
+Vector of genes.
+}
+\description{
+Read OncoKB
+}
diff --git a/tests/testthat/test-roxytest-testexamples-purple.R b/tests/testthat/test-roxytest-testexamples-purple.R
index 3f83ec0..528f853 100644
--- a/tests/testthat/test-roxytest-testexamples-purple.R
+++ b/tests/testthat/test-roxytest-testexamples-purple.R
@@ -19,7 +19,7 @@ test_that("Function purple_cnv_som_gene_process() @ L60", {
 })
 
 
-test_that("Function purple_cnv_som_read() @ L444", {
+test_that("Function purple_cnv_som_read() @ L449", {
   
   x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
   (p <- purple_cnv_som_read(x))
@@ -27,7 +27,7 @@ test_that("Function purple_cnv_som_read() @ L444", {
 })
 
 
-test_that("Function purple_cnv_som_process() @ L477", {
+test_that("Function purple_cnv_som_process() @ L482", {
   
   x <- system.file("extdata/purple/purple.cnv.somatic.tsv", package = "gpgr")
   (pp <- purple_cnv_som_process(x))
@@ -35,7 +35,7 @@ test_that("Function purple_cnv_som_process() @ L477", {
 })
 
 
-test_that("Function purple_qc_read() @ L545", {
+test_that("Function purple_qc_read() @ L550", {
   
   x <- system.file("extdata/purple/purple.qc", package = "gpgr")
   (q <- purple_qc_read(x))
@@ -43,7 +43,7 @@ test_that("Function purple_qc_read() @ L545", {
 })
 
 
-test_that("Function purple_purity_read() @ L603", {
+test_that("Function purple_purity_read() @ L608", {
   
   x <- system.file("extdata/purple/purple.purity.tsv", package = "gpgr")
   (p <- purple_purity_read(x))

From 327f170424acaca503dd7b0626af3873322d8622 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Tue, 7 May 2024 09:49:32 +1000
Subject: [PATCH 8/8] can use dplyr instead of tidyselect

---
 DESCRIPTION            | 3 +--
 R/purple.R             | 4 ++--
 R/sv.R                 | 4 ++--
 conda/recipe/meta.yaml | 2 --
 4 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index dfc9657..e06fa33 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -43,8 +43,7 @@ Suggests:
     scales,
     sigrap,
     testthat (>= 3.0.0),
-    tibble,
-    tidyselect,
+    tibble
 Roxygen: list(markdown = TRUE,
               roclets = c("namespace", "rd", "roxytest::testthat_roclet"))
 biocViews:
diff --git a/R/purple.R b/R/purple.R
index 1046aa4..16c00f3 100644
--- a/R/purple.R
+++ b/R/purple.R
@@ -643,7 +643,7 @@ purple_purity_read <- function(x) {
 
   purple_purity <- purple_purity |>
     dplyr::mutate(
-      dplyr::across(tidyselect::where(is.numeric), \(x) round(x, 2)),
+      dplyr::across(dplyr::where(is.numeric), \(x) round(x, 2)),
       dplyr::across(dplyr::everything(), as.character)
     ) |>
     tidyr::pivot_longer(dplyr::everything(), names_to = "column", values_to = "value") |>
@@ -745,7 +745,7 @@ purple_kataegis <- function(x) {
 
   data <- d$data |>
     dplyr::filter(!is.na(.data$KT)) |>
-    dplyr::select(c("CHROM", "POS", tidyselect::all_of(info_cols)))
+    dplyr::select(c("CHROM", "POS", dplyr::all_of(info_cols)))
 
   description <- d$description |>
     dplyr::filter(.data$ID %in% info_cols) |>
diff --git a/R/sv.R b/R/sv.R
index 6a4ede5..1803bee 100644
--- a/R/sv.R
+++ b/R/sv.R
@@ -29,9 +29,9 @@ split_double_col <- function(d, nms) {
   assertthat::assert_that(is.character(nms))
 
   outd <- d |>
-    dplyr::select(tidyselect::all_of(nms)) |>
+    dplyr::select(dplyr::all_of(nms)) |>
     dplyr::mutate(num = dplyr::row_number()) |>
-    tidyr::pivot_longer(cols = tidyselect::all_of(nms), names_to = "col_nm", values_to = "x1_x2") |>
+    tidyr::pivot_longer(cols = dplyr::all_of(nms), names_to = "col_nm", values_to = "x1_x2") |>
     tidyr::separate(.data$x1_x2, into = c("x1", "x2"), sep = ",", fill = "right") |>
     dplyr::mutate(
       x1 = round(as.double(.data$x1), 2),
diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
index 23a2291..2a58a59 100644
--- a/conda/recipe/meta.yaml
+++ b/conda/recipe/meta.yaml
@@ -43,7 +43,6 @@ requirements:
     - r-scales
     - r-testthat
     - r-tibble
-    - r-tidyselect
 
   run:
     - r-base
@@ -73,7 +72,6 @@ requirements:
     - r-scales
     - r-testthat
     - r-tibble
-    - r-tidyselect
 
 test:
   commands: