fragLen_calcStranded {seqsetvis} | R Documentation

## calculate fragLen from a bam file for specified regions

### Description

calculate fragLen from a bam file for specified regions

### Usage

    fragLen_calcStranded(
      bam_f,
      qgr,
      n_regions = 100,
      include_plot_in_output = FALSE,
      test_fragLen = seq(100, 400, 5),
      flip_strand = FALSE,
      ...
    )

### Arguments

`bam_f` | character or BamFile. bam file to read from. .bai index file must be in same directory
`qgr` | GRanges. used as which for ScanBamParam. Can be NULL if it's REALLY important to load the entire bam, force_no_which = TRUE also required.
`n_regions` | numeric (integer) it's generally overkill to pull all regions at this stage and will slow calculation down. Default is 100.
`include_plot_in_output` | if TRUE ouptut is a list of fragLen and a ggplot showing values considered by calculation. Default is FALSE.
`test_fragLen` | numeric. The set of fragment lenghts to gather strand cross correlation for.
`flip_strand` | boolean. if TRUE strands that reads align to are swapped. This is typically only necessary if there was a mismatch between library chemistry and aligner settings. Default is FALSE.
`...` | passed to Rsamtools::ScanBamParam, can't be which or what.

### Value

numeric fragment length

### Examples

    bam_file = system.file("extdata/test.bam",
        package = "seqsetvis")
    qgr = CTCF_in_10a_overlaps_gr[1:5]
    fragLen_calcStranded(bam_file, qgr)
    #if plot is included, a list is returned, item 2 is the plot
    fragLen_calcStranded(bam_file, qgr,
      include_plot_in_output = TRUE)[[2]]

[Package seqsetvis version 1.10.0 Index]