quietVDJ

DESCRIPTION

@@ -33,6 +33,7 @@ Imports:
     rjson,
     rlang,
     S4Vectors,
+    Seurat,
     SeuratObject,
     SingleCellExperiment,
     stats,
@@ -55,7 +56,6 @@ Suggests:
     rmarkdown,
     scales,
     scater,
-    Seurat,
     spelling,
     testthat (>= 3.0.0),
     vdiffr

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(quietBCRgenes,default)
+S3method(quietTCRgenes,Seurat)
+S3method(quietTCRgenes,default)
 export(StartracDiversity)
 export(addVariable)
 export(alluvialClones)
@@ -27,6 +30,7 @@ export(exportClones)
 export(expression2List)
 export(getCirclize)
 export(getContigDoublets)
+export(getHumanIgPseudoGenes)
 export(highlightClones)
 export(loadContigs)
 export(percentAA)
@@ -35,11 +39,15 @@ export(percentKmer)
 export(percentVJ)
 export(positionalEntropy)
 export(positionalProperty)
+export(quietBCRgenes)
+export(quietTCRgenes)
+export(quietVDJgenes)
 export(subsetClones)
 export(vizGenes)
 import(ggplot2)
 importFrom(Rcpp,sourceCpp)
 importFrom(S4Vectors,DataFrame)
+importFrom(SeuratObject,"VariableFeatures<-")
 importFrom(SeuratObject,Embeddings)
 importFrom(SeuratObject,Idents)
 importFrom(SingleCellExperiment,colData)

R/quietVDJ.R

@@ -0,0 +1,139 @@
+#' Remove TCR and BCR genes from variable gene results
+#'
+#' @description
+#' `r lifecycle::badge("experimental")`
+#'
+#' Most single-cell workflows use highly-expressed and highly-variable
+#' genes for the initial calculation of PCA and subsequent dimensional
+#' reduction. This function will remove the TCR and/or BCR genes from the
+#' variable features in a Seurat object or from a vector (potentially
+#' generated by the Bioconductor scran workflow).
+#'
+#' @examples
+#' example <- quietVDJgenes(scRep_example)
+#' trex_example <- quietTCRgenes(scRep_example)
+#' ibex_example <- quietBCRgenes(scRep_example)
+#'
+#' @param sc Single-cell object in Seurat format or vector of variable genes
+#' to use in reduction
+#' @param assay The Seurat assay slot to use to remove immune receptor genes
+#' from, NULL value will default to the default assay
+#'
+#' @importFrom SeuratObject VariableFeatures<-
+#' @export
+#' @return Seurat object or vector list with TCR genes removed.
+quietVDJgenes <- function(sc, ...) {
+    quietTCRgenes(quietBCRgenes(sc, ...))
+}
+
+#' @rdname quietVDJgenes
+#' @export
+#' @author Nicky de Vrij, Nikolaj Pagh, Nick Borcherding, Qile Yang
+quietTCRgenes <- function(sc, ...) {
+    UseMethod("quietTCRgenes")
+}
+
+#' @rdname quietVDJgenes
+#' @method quietTCRgenes default
+#' @export
+quietTCRgenes.default <- function(sc, ...) {
+    assert_that(is.character(sc))
+    unwanted_genes <- grep("^TR[ABDG][VDJ][^D]", x = sc, value = TRUE)
+    sc[sc %!in% unwanted_genes]
+}
+
+#' @rdname quietVDJgenes
+#' @method quietTCRgenes Seurat
+#' @export
+quietTCRgenes.Seurat <- function(sc, assay = NULL, ...) {
+    if (is.null(assay)) {
+        assay <- DefaultAssay(sc)
+    }
+    VariableFeatures(sc, assay = assay) <-
+        quietTCRgenes.default(SeuratObject::VariableFeatures(sc, assay = assay))
+    sc
+}
+
+#' @rdname quietVDJgenes
+#' @export
+quietBCRgenes <- function(sc, ...) {
+    UseMethod("quietBCRgenes")
+}
+
+#' @rdname quietVDJgenes
+#' @method quietBCRgenes default
+#' @export
+quietBCRgenes.default <- function(sc, ...) {
+    assert_that(is.character(sc))
+    unwanted_genes <- c(grep("^IG[HLK][VDJCAGM]", sc, value = TRUE), "JCHAIN")
+    unwanted_genes <- unwanted_genes[
+        unwanted_genes %!in% getHumanIgPseudoGenes()
+    ]
+    sc[sc %!in% unwanted_genes]
+}
+
+#' @rdname quietVDJgenes
+#' @method quietBCRgenes default
+#' @export
+quietBCRgenes.Seurat <- function(sc, assay = NULL) {
+    if (is.null(assay)) {
+        assay <- DefaultAssay(sc)
+    }
+    VariableFeatures(sc, assay = assay) <-
+        quietBCRgenes.default(SeuratObject::VariableFeatures(sc, assay = assay))
+    sc
+}
+
+#' Get Human Immunoglobulin pseudogenes
+#'
+#' This function returns a character vector of human immunoglobulin
+#' pseudogenes. These are also the genes that are removed from the
+#' variable gene list in [quietBCRgenes()] and [quietVDJgenes()].
+#'
+#' @return Character vector of human immunoglobulin pseudogenes.
+#' @export
+#'
+getHumanIgPseudoGenes <- function() {
+    unique(c(
+        "IGHJ1P", "IGHJ2P", "IGHJ3P", "IGLC4", "IGLC5", "IGHEP1", "IGHEP2",
+        "IGHV1-12","IGHV1-14", "IGHV1-17", "IGHV1-67", "IGHV1-68",
+        "IGHV2-10", "IGHV3-6", "IGHV3-19", "IGHV3-22", "IGHV3-25",
+        "IGHV3-29", "IGHV3-32", "IGHV3-36", "IGHV3-37", "IGHV3-41",
+        "IGHV3-42", "IGHV3-47", "IGHV3-50", "IGHV3-52", "IGHV3-54",
+        "IGHV3-57", "IGHV3-60", "IGHV3-62", "IGHV3-63", "IGHV3-65",
+        "IGHV3-71", "IGHV3-75", "IGHV3-76", "IGHV3-79", "IGHV4-55",
+        "IGHV4-80", "IGHV5-78", "IGHV7-27", "IGHV7-40", "IGHV7-56", 
+        "IGHVIII-44", "IGHVIII-82", "IGKV1-22", "IGKV1-32", "IGKV1-35",
+        "IGKV1D-22", "IGKV1D-27", "IGKV1D-32", "IGKV1D-35", "IGKVOR-2",
+        "IGKVOR-3", "IGKVOR-4", "IGKV2-4", "IGKV2-10", "IGKV2-14", "IGKV2-18",
+        "IGKV2-19", "IGKV2-23", "IGKV2-26", "IGKV2-36", "IGKV2-38",
+        "IGKV2D-10", "IGKV2D-14", "IGKV2D-18", "IGKV2D-19", "IGKV2D-23",
+        "IGKV2D-36", "IGKV2D-38", "IGKV3-25", "IGKV3-31", "IGKV3-34",
+        "IGKV7-3", "IGLCOR22-1", "IGLCOR22-2", "IGLJCOR18", "IGLV1-41", 
+        "IGLV1-62", "IGLV2-5", "IGLV2-28", "IGLV2-34", "IGLV3-2", 
+        "IGLV3-4", "IGLV3-6", "IGLV3-7", "IGLV3-13", "IGLV3-15",
+        "IGLV3-17", "IGLV3-24", "IGLV3-26", "IGLV3-29", "IGLV3-30",
+        "IGLV3-31", "IGLV7-35", "IGLV10-67", "IGLVI-20", "IGLVI-38",
+        "IGLVI-42", "IGLVI-56", "IGLVI-63", "IGLVI-68", "IGLVI-70", 
+        "IGLVIV-53", "IGLVIV-59", "IGLVIV-64", "IGLVIV-65", "IGLVV-58",
+        "IGLVV-66", "IGHV1OR15-2", "IGHV1OR15-3", "IGHV1OR15-4", "IGHV1OR15-6",
+        "IGHV1OR16-1", "IGHV1OR16-2", "IGHV1OR16-3", "IGHV1OR16-4", "IGHV3-30-2", 
+        "IGHV3-33-2", "IGHV3-69-1", "IGHV3OR15-7", "IGHV3OR16-6", "IGHV3OR16-7",
+        "IGHV3OR16-11", "IGHV3OR16-14", "IGHV3OR16-15", "IGHV3OR16-16", "IGHV7-34-1",
+        "IGHVII-1-1", "IGHVII-15-1", "IGHVII-20-1", "IGHVII-22-1", "IGHVII-26-2",
+        "IGHVII-28-1", "IGHVII-30-1", "IGHVII-30-21", "IGHVII-31-1", "IGHVII-33-1", 
+        "IGHVII-40-1", "IGHVII-43-1", "IGHVII-44-2", "IGHVII-46-1", "IGHVII-49-1",
+        "IGHVII-51-2", "IGHVII-53-1", "IGHVII-60-1", "IGHVII-62-1", "IGHVII-65-1", 
+        "IGHVII-67-1", "IGHVII-74-1", "IGHVII-78-1", "IGHVIII-2-1", "IGHVIII-5-1",
+        "IGHVIII-5-2", "IGHVIII-11-1", "IGHVIII-13-1", "IGHVIII-16-1", "IGHVIII-22-2",
+        "IGHVIII-25-1", "IGHVIII-26-1", "IGHVIII-38-1", "IGHVIII-47-1", "IGHVIII-67-2",
+        "IGHVIII-67-3", "IGHVIII-67-4", "IGHVIII-76-1", "IGHVIV-44-1", "IGKV1OR1-1", 
+        "IGKV1OR2-1", "IGKV1OR2-2", "IGKV1OR2-3", "IGKV1OR2-6", "IGKV1OR2-9",
+        "IGKV1OR2-11", "IGKV1OR2-118", "IGKV1OR9-1", "IGKV1OR9-2", "IGKV1OR10-1", 
+        "IGKV1OR15-118", "IGKV1OR22-1", "IGKV1OR22-5", "IGKV1ORY-1", "IGKV2OR2-1",
+        "IGKV2OR2-2", "IGKV2OR2-4", "IGKV2OR2-7", "IGKV2OR2-7D", "IGKV2OR2-8",
+        "IGKV2OR2-10", "IGKV2OR22-3", "IGKV2OR22-4", "IGKV3OR2-5", "IGKV3OR22-2",
+        "IGKV8OR8-1", "IGLVIV-66-1", "IGLVIVOR22-1", "IGLVIVOR22-2", "IGLVVI-22-1", 
+        "IGLVVI-25-1", "IGLVVII-41-1"
+    ))
+}