read_bamfile: Read a bam file Read a bam file from give path. Alignment and...

In Pitithat-pu/cfdnakit: Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)

Read a bam file Read a bam file from give path. Alignment and sequencing read information will be binned into non-overlapping size

Description

Read a bam file Read a bam file from give path. Alignment and sequencing read information will be binned into non-overlapping size

Usage

read_bamfile(
  bamfile_path,
  binsize = 1000,
  blacklist_files = NULL,
  genome = "hg19",
  target_bedfile = NULL,
  min_mapq = 20,
  apply_blacklist = TRUE
)

Arguments

bamfile_path	Character; Path to sample bamfile
binsize	Int; Size of non-overlapping windows in KB. Only 100,500 and 1000 is available; Default 1000
blacklist_files	Character; Filepath to file containing blacklist regions
genome	Character; abbreviation of reference genome; available genome: hg19,hg38, mm10. default:hg19
target_bedfile	Character; Path to exon/target bedfile; Default NULL
min_mapq	Int; minimum read mapping quality; Default 20
apply_blacklist	Logical; To exclude read on the blacklist regions Default TRUE

Value

SampleBam Object; A list object containing read information from the BAM file.

Examples

fl <- system.file("extdata","ex.plasma.bam",package = "cfdnakit")
### read bam file with default params (hg19, 1000K binsize)
sample.bam <-read_bamfile(fl, apply_blacklist=FALSE)

Pitithat-pu/cfdnakit documentation built on April 5, 2024, 8:50 p.m.