get_bam_bed: Get bam file directories, sample names, and whole genomic...

In rujinwang/SCOPE: A normalization and copy number estimation method for single-cell DNA sequencing

Get bam file directories, sample names, and whole genomic bins

Description

Get bam file directories, sample names, and whole genomic bins from .bed file

Usage

get_bam_bed(bamdir, sampname, hgref = "hg19", resolution = 500, 
            sex = FALSE)

Arguments

bamdir	vector of the directory of a bam file. Should be in the same order as sample names in sampname.
sampname	vector of sample names. Should be in the same order as bam directories in bamdir.
hgref	reference genome. This should be 'hg19', 'hg38' or 'mm10'. Default is human genome hg19.
resolution	numeric value of fixed bin-length. Default is 500. Unit is "kb".
sex	logical, whether to include sex chromosomes. Default is FALSE.

Value

A list with components

bamdir	A vector of bam directories
sampname	A vector of sample names
ref	A GRanges object specifying whole genomic bin positions

Author(s)

Rujin Wang [e-mail]

Examples

library(WGSmapp)
library(BSgenome.Hsapiens.UCSC.hg38)
bamfolder <- system.file('extdata', package = 'WGSmapp')
bamFile <- list.files(bamfolder, pattern = '*.dedup.bam$')
bamdir <- file.path(bamfolder, bamFile)
sampname_raw <- sapply(strsplit(bamFile, '.', fixed = TRUE), '[', 1)
bambedObj <- get_bam_bed(bamdir = bamdir, sampname = sampname_raw, 
                        hgref = "hg38")
bamdir <- bambedObj$bamdir
sampname_raw <- bambedObj$sampname
ref_raw <- bambedObj$ref

rujinwang/SCOPE documentation built on Jan. 1, 2023, 5:40 a.m.