Remove BuenRTools dependency

splitAndFetch <- function (vec, delim, part) 

{

  if (length(part) == 1) {

    sapply(strsplit(as.character(vec), delim, fixed = TRUE), 

           "[[", part)

  }

  else {

    sapply(strsplit(as.character(vec), delim, fixed = TRUE), 

           function(x) paste(x[part], collapse = delim))

  }

}

geneCorr <- function(ATAC, # ATAC feature (e.g., Footprint or CRE) RangedSummarizedExperiment

                     RNA, # Gene-by-pseudobulk (or -by-single cell) matrix of RNA. Should be log-normalized

                     genome, # Must be one of "hg19", "mm10", or "hg38"

  if (!genome %in% c("hg19", "hg38", "mm10")) 

    stop("You must specify one of hg19, hg38 or mm10 as a genome build for currently supported TSS annotations..\n")

  switch(genome, hg19 = {

    TSSg <- BuenRTools::hg19TSSRanges

    TSSg <- FigR::hg19TSSRanges

  }, hg38 = {

    TSSg <- BuenRTools::hg38TSSRanges

    TSSg <- FigR::hg38TSSRanges

  }, mm10 = {

    TSSg <- BuenRTools::mm10TSSRanges

    TSSg <- FigR::mm10TSSRanges

  })

  # Keep genes that have annotation 

  # Swap feature numbers to match reference input feature numbers

  # This only changes if some features had zero signal and were filtered out

  # Use rownames from reference

  corrResults$Feature <- as.numeric(BuenRTools::splitAndFetch(rownames(ATACmat)[corrResults$Feature],"Feature",2))

  corrResults$Feature <- as.numeric(splitAndFetch(rownames(ATACmat)[corrResults$Feature],"Feature",2))

  cat("\nFinished!\n")