cnvReadBam: Wrapper to Rsamtools:scanBam to load .bam file as a...

In daynefiler/mcCNV: Call copy number variants from whole exome/whole genome sequencing data

Description

cnvReadBam serves as a wrapper to call Rsamtools:scanBam and processes the list result into a data.table.

Usage

cnvReadBam(
  bamfile,
  which,
  what = scanBamWhat(),
  flag = scanBamFlag(),
  tags = NULL,
  keyby = NULL
)

Arguments

bamfile	Character of length 1, the file path to the .bam file
which	IRangesList or GRanges object, the range of sequences to load, passed to Rsamtools::ScanBamParam 'which' parameter; loads all sequences when omitted
what	Character, the fields to extract from the bam file, passed to Rsamtools::ScanBamParam 'what' parameter
tags	Character, the tag fields to extract from the bam file, passed to Rsamtools::ScanBamParam 'tags' parameter
keyby	Character, the field to key the data.table by

Value

data.table object with specified fields & tags extracted from .bam file

daynefiler/mcCNV documentation built on Dec. 15, 2021, 3:58 a.m.