countParam: Generate parameters that specify which reads in a bam file to...

In cancer-genomics/trellis: Somatic structural variant analysis

Generate parameters that specify which reads in a bam file to import

Description

A wrapper function for Rsamtools::ScanBamParam().

Usage

countParam(
  gr,
  flags = scanBamFlag(isUnmappedQuery = FALSE, isDuplicate = FALSE)
)

Arguments

gr	A GRanges object
flags	An integer vector as returned by Rsamtools::scanBamFlag(). Unmapped and duplicate reads are omitted by default.

Value

A ScanBamParam object

Examples

library(Rsamtools)
library(svfilters.hg19)
data(bins1kb)
scan_param <- countParam(bins1kb)
scan_param
class(scan_param) #ScanBamParam

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.