crossCorrByRle {seqsetvis} | R Documentation

## Calculate cross correlation by using shiftApply on read coverage Rle

### Description

Calculate cross correlation by using shiftApply on read coverage Rle

### Usage

    crossCorrByRle(
      bam_file,
      query_gr,
      max_dupes = 1,
      fragment_sizes = 50:300,
      read_length = NULL,
      flip_strand = FALSE,
      ...
    )

### Arguments

`bam_file` | character. Path to .bam file, must have index at .bam.bai.
`query_gr` | GRanges. Regions to calculate cross correlation for.
`max_dupes` | integer. Duplicate reads above this value will be removed.
`fragment_sizes` | integer. fragment size range to search for maximum correlation.
`read_length` | integer. Any values outside fragment_range that must be searched. If not supplied will be determined from bam_file. Set as NA to disable this behavior.
`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.
`...` | arguments passed to ScanBamParam

### Value

named list of results

### Examples

    bam_f = system.file("extdata/test.bam",
        package = "seqsetvis", mustWork = TRUE)
    query_gr = CTCF_in_10a_overlaps_gr[1:2]
    crossCorrByRle(bam_f, query_gr[1:2], fragment_sizes = seq(50, 300, 50))

[Package seqsetvis version 1.10.0 Index]