R/overlapPos.R

In quevedor2/CCLid: Compares Cancer Cell Line Genotypes Against Pharmacogenomic Datasets

#' overlapPos
#' @description parent function that handles how overlaps are done between COMParing 
#' group and REFerence datasets
#' 
#' @param comp Input comparison data with a $Probe_Set_ID column
#' @param ref Reference probeset order where rownames are Probe_Set_IDs
#' @param mapping If "probeset", will using $Probe_Set_ID from comp dataframe.
#' @param snp6.dat SNP6 probeset genomic position, accessible from CCLid::ccl_table
#' Else, it will use the rownames of ref as the probe set IDs
#'
#' @export
overlapPos <- function(comp, ref, mapping='probeset', snp6.dat){
  switch(mapping,
         "probeset"={
           if(any(grepl("Probe_Set_ID", colnames(comp)))){
             .overlapProbeset(ref.ids=rownames(ref), 
                              comp.ids=comp$Probe_Set_ID, 
                              snp6.dat=snp6.dat)
           } else {
             .overlapProbeset(ref.ids=rownames(ref), 
                              comp.ids=rownames(comp), 
                              snp6.dat=snp6.dat)
           }
           })
}

#' findCclPairs
#' @description Finds indices for cell lines that are found
#' in multiple datasets
#' 
#' @param meta.df Metadata containing cell IDs and their dataset mapping
#' @param dr.nm  matrix where column names are cell lines/datasets
#' @param ds Dataset (if any) to return (e.g. c('CCLE', 'GDSC'))
#' @importFrom stats setNames
#' 
#' @return A list of indices indicating pair of cell lines for the data matrix
#' @export
findCclPairs <- function(meta.df, dr.nm, ds=NULL){
  all.idx <- sapply(meta.df$ID, function(i) {
    id <- grep(paste0("_", i, "$"), x=colnames(dr.nm))
    id <- setNames(id, colnames(dr.nm)[id])
    if(!is.null(ds)){
      #ds <- c('CCLE', 'GDSC')
      id[grep(paste(ds, collapse="|"), names(id))]
    } else {
      id
    }
  })
  return(all.idx)
}