ReadSignatures: Read signatures in .gmt format

In nbroguiere/burgertools: Collection of tools extending the functionality of Seurat

Read signatures in .gmt format

Description

This function reads signatures in the .gmt format and returns them as a named list.

Usage

ReadSignatures(file, discard.comments = TRUE)

Arguments

file	character(1). The address/name of the file from which signatures are read.
discard.comments	logical(1). Whether the comment column of the gmt file should be discarded. Default: TRUE.

Value

Returns a mamed list of chr vectors, in which the names of the list elements are the signature names, and the chr vectors are the corresponding gene collections. If discard comments=FALSE, will return a list of two in which the first element are the signatures, and the second element the comments.

Examples

signature.list <- list()
signature.list[["TC"]] <- c("CD3D","CD3E","CD3G","CD4","CD8A","CD8B","GZMA","IFNG","NCAM1","KLRK1","JAK3")
signature.list[["BC"]] <- c("IGHM","CD79A","CD79B","MZB1","DERL3","IGLL5","MS4A1","IGHD","IGHG1","IGHG3")
signature.list[["MP"]] <- c("CD74","HLA-DRA","HLA-DRB1","CD68","ITGAX","CD14","FCGR1A","MRC1","LYZ")
signature.list[["EP"]] <- c("EPCAM","PHGR1","TFF3","CKB","AGR2","PLCG2","CDX2","PIGR","PHGR1","CD24","LGALS4","GPX2","CEACAM6","CLDN3","KRT8","KRT19","KRT18","TSPAN8","OLFM4","FABP1","REG1A")
signature.list[["CAF"]]<- c("LOXL2","TAGLN","COL6A1","ITGA1","MMP1","MMP3","ACTA2","COL1A1","CALD1","COL3A1","COL1A2","COL6A3","COL6A2","THY1","DCN","COL5A2","COL5A1","PDGFRB")
signature.list[["EC"]] <- c("CD34","PECAM1","LYVE1","PLVAP","RAMP2","VWF","ESM1","FLT1","PODXL","GNG11","ENG","SLC9A3R2","HSPG2")
WriteSignatures(signature.list,"MyFile.gmt")
signature.list2 <- ReadSignatures("MyFile.gmt")
library(zeallot)
c(signature.list2,comments) %<-% ReadSignatures("MyFile.gmt",discard.comments=F)

nbroguiere/burgertools documentation built on Jan. 30, 2024, 3:48 a.m.