R/gene_map_functions.R

In joshuamschmidt/multiPermr: What the Package Does in One 'Title Case' Line

map_to_genes <- function(dt,genesdt,groupid){
  data.table::setkey(dt,chr,start,end)
  data.table::setkey(genesdt,chr,start,end)
  geneDT <- data.table::foverlaps(dt,genesdt,nomatch = 0)[order(gene)][,.(group=groupid,gene=unique(gene))]
  return(geneDT)
}

map_stats_to_genes <- function(stats=list('s1','s2'),
                               genes){
  mapped_stats <- rbindlist(lapply(seq_along(stats), function(y, n, i) map_to_genes(dt=y[[i]],genesdt=genes,groupid=n[[i]]), y=stats, n=names(stats)))
  return(mapped_stats)
}