R/subset_ex_sc.R

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

#' This will setset your expression set by some variable in pData
#'
#' This function will take an input ex_sc and produce a subsetted one preserving all metadata
#'
#' @param input the input ex_sc
#' @param variable the variable of pData to select on
#' @param select the value or values to subset
#' @export
#' @details
#' By providing both a variable, and a selecting argument, only cells of of a certain condition will be selected
#' @examples
#' subset_ex_sc(ex_sc_example, variable = "Cluster", select = c("Cluster1"))

subset_ex_sc <- function(input, variable, select){
 dat <- pData(input)
 ind <- match(variable, colnames(dat))
 val <- dat[,ind]
 selected <- c()
 for(s in select){
   ind2 <- grep(paste0("^", s, "$"), val)
   selected <- c(selected, ind2)
 }
 cells <- rownames(dat)[selected]
 subset <- input[,cells]
 print(paste0("Subsetted Data is ", length(cells), " cells"))
 print(table(pData(subset)[,variable]))
 return(subset)
}