From f70b99e98888700c336f5c1d0cd03aa22be97317 Mon Sep 17 00:00:00 2001 From: qclayssen Date: Fri, 15 Nov 2024 10:04:48 +1100 Subject: [PATCH] Change documention --- inst/rmd/umccrise/cancer_report.Rmd | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/inst/rmd/umccrise/cancer_report.Rmd b/inst/rmd/umccrise/cancer_report.Rmd index 9f7b4a3..c5124af 100644 --- a/inst/rmd/umccrise/cancer_report.Rmd +++ b/inst/rmd/umccrise/cancer_report.Rmd @@ -303,11 +303,8 @@ summarise_sigs <- function(mut_sig_contr) { snv_summary_counts <- params$somatic_snv_summary |> jsonlite::read_json() -# NOTE(SW): hypermutated status is determine indirectly by different counts between 'sage' and -# 'annotated' since this indicates that the bolt hypermutated logic evaluated as true and applied -# variant selection - -hypermutated <- snv_summary_counts$sage > 500000 +# NOTE(QC): samples are considered hypermutated if they have more than 500k variant +hypermutated <- snv_summary_counts$annotated > 500000 snv_summary <- snv_summary_counts |> unlist() |> @@ -355,8 +352,7 @@ qc_summary_all <- dplyr::tribble( ~n, ~variable, ~value, ~details, 4, "Hypermutated", ifelse(hypermutated, "TRUE", "FALSE"), ifelse(hypermutated, glue::glue( - "More than 500K SNVs detected (including non-PASS), priority regions and/or variants ", - "selected for processing.", + "More than 500K SNVs detected (including non-PASS)", ), ""), 5, "MutSigs (Old)", glue::glue("{summarise_sigs(sigs_snv_2015)}"), "2015 COSMIC (https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt)",