ssvFetchBam.single {seqsetvis} | R Documentation |
fetch a windowed version of a bam file, returns GRanges
ssvFetchBam.single(bam_f, qgr, win_size = 50, win_method = c("sample", "summary")[1], summary_FUN = stats::weighted.mean, fragLen = NULL, target_strand = c("*", "+", "-")[1], anchor = c("left", "left_unstranded", "center", "center_unstranded")[3], return_data.table = FALSE)
bam_f |
character or BamFile to load |
qgr |
GRanges regions to fetchs |
win_size |
numeric >=1. pileup grabbed every win_size bp for win_method sample. If win_method is summary, this is the number of windows used (confusing, sorry). |
win_method |
character. one of c("sample", "summary"). Determines
if |
summary_FUN |
function. only relevant if win_method is "summary".
passed to |
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 accordingly. ignored if any other value. |
anchor |
character, one of c("center", "center_unstranded", "left", "left_unstranded") |
return_data.table |
logical. If TRUE the internal data.table is returned instead of GRanges. Default is FALSE. |
tidy GRanges (or data.table if specified) with pileups from bam file. pileup is calculated only every win_size bp.
bam_file = system.file("extdata/test.bam", package = "seqsetvis") qgr = CTCF_in_10a_overlaps_gr[1:5] bam_gr = ssvFetchBam.single(bam_file, qgr) bam_gr = ssvFetchBam.single(bam_file, qgr, fragLen = 180, win_size = 10, target_strand = "+") bam_dt = ssvFetchBam.single(bam_file, qgr, return_data.table = TRUE)