R/WriteSignatures.R

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

#' Write signatures in .gmt format
#'
#' This function writes signature lists in the [.gmt format](https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29).
#' @param signatures Named list of character vectors, in which the names of the list elements are the signature names, and the chr vectors are the corresponding gene collections.
#' @param file character(1). The address/name of the file from which signatures are read.
#' @param comment character(n). What should be written in the comment second column in the gmt file. Recycled circularly if less than the number of signatures. Default: "cell type gene signature".
#' @param append logical(1). Should the signatures be appended to an existing file rather than overwrite. Default: FALSE.
#' @keywords write signatures gmt .gmt gene matrix transpose
#' @export
#' @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")

WriteSignatures <- function(signature.list,file,comment="cell type gene signature",append=F){
  if(length(comment)<length(signature.list)){
    comment <- rep(comment, length(signature.list))
  }
  for(i in 1:length(signature.list)){
    readr::write_tsv(as.data.frame(t(as.matrix(c(names(signature.list)[i],comment[i],signature.list[[i]])))),file,append = append,col_names = F)
    append <- T
  }
}