ssvFetchBam.single {seqsetvis} | R Documentation

## fetch a windowed version of a bam file, returns GRanges

### Description

fetch a windowed version of a bam file, returns GRanges

### Usage

    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)

### Arguments

`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 `viewGRangesWinSample_dt` or `viewGRangesWinSummary_dt` is used to represent each region in qgr.
`summary_FUN` | function. only relevant if win_method is "summary". passed to `viewGRangesWinSummary_dt`.
`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.

### Value

tidy GRanges (or data.table if specified) with pileups from bam file. pileup is calculated only every win_size bp.

### Examples

    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)

[Package seqsetvis version 1.0.2 Index]