fetchBam {seqsetvis} | R Documentation

## fetch a bam file pileup with the ability to consider cross strand correlation

### Description

fetch a bam file pileup with the ability to consider cross strand correlation

### Usage

    fetchBam(bam_f, qgr, fragLen = NULL, target_strand = c("*", "+", "-")[1],
      ...)

### Arguments

`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.

### Value

GRanges containing tag pileup values in score meta column. tags are optionally extended to fragment length (fragLen) prior to pile up.

### Examples

    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 = "+")

[Package seqsetvis version 1.0.2 Index]