Provided input and signal sorted/indexed bams, subset to specified region and store as temp file. about peakpeeker HOT 1 CLOSED

library(Rsamtools)
library(GenomicRanges)

gr <- GRanges(seqnames = "chr12",
              ranges = IRanges(start = c(6522378), end = c(6769097)))

bammy <- BamFile("A549_H3K27AC.ENCFF872MQN.sorted.bam", index = "A549_H3K27AC.ENCFF872MQN.sorted.bam.bai")

params <- ScanBamParam(which = gr, what = scanBamWhat())

start.time <- Sys.time()

filterBam(bammy, destination = "A549_H3K27AC.ENCFF872MQN.250k.sorted.bam", index = bammy, param = params)

end.time <- Sys.time()

end.time - start.time