.getinput <- function(parameter) {
## get merippp
if (length(parameter$exomepeak_input) == 1) {
exomepeak_input <- .getexomepeakinput(parameter$peak_bed, parameter)
parameter$exomepeak_input <- exomepeak_input
}
input <- .makeInput(parameter, extend = 50, min_reads = 5)
input$exomePeak_filter <- parameter$exomepeak_input$id!=0
save(input, file = paste(parameter$output_filepath, "input.RData", sep = "/"))
return(input)
}
.getexomepeakinput <- function(peak_bed, parameter) {
meripp <- BED12toGRangesList(peak_bed)
id <- countOverlaps(meripp, parameter$tx_genes, type = "within")
meripp <- meripp[id!=0]
print("Cutting peak to Single Base...")
tic <- Sys.time()
peakSB <- .makePeak2SB(meripp, parameter$tx_genes, extend = 50)
print(Sys.time() - tic)
## get motif info
print("Searching peak for motifs...")
tic <- Sys.time()
peakMF <- .makePeak2Motif(meripp, parameter, extend = 50)
print(Sys.time() - tic)
return(list(meripp = meripp, id = id, peakSB = peakSB, peakMF = peakMF))
}
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