fetchBam {seqsetvis} | R Documentation |
fetch a bam file pileup with the ability to consider cross strand correlation
fetchBam(bam_f, qgr, fragLen = NULL, target_strand = c("*", "+", "-")[1], ...)
bam_f |
character or BamFile to load |
qgr |
GRanges regions to fetchs |
fragLen |
numeric, NULL, or NA. if numeric, supplied value is used. if NULL, value is calculated with fragLen_calcStranded if NA, raw bam pileup with no cross strand shift is returned. |
target_strand |
character. if one of "+" or "-", reads are filtered to match. ignored if any other value. |
... |
passed to ScanBamParam(), can't be which or what. |
GRanges containing tag pileup values in score meta column. tags are optionally extended to fragment length (fragLen) prior to pile up.
bam_file = system.file("extdata/test.bam", package = "seqsetvis") qgr = CTCF_in_10a_overlaps_gr[1:5] fetchBam(bam_file, qgr) fetchBam(bam_file, qgr, fragLen = 180, target_strand = "+")