get_samp_QC: Get QC metrics for single cells

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

Description

Perform QC step on single cells.

Usage

get_samp_QC(bambedObj)

Arguments

bambedObj

object returned from get_bam_bed

Value

QCmetric

A matrix containing total number/proportion of reads, total number/proportion of mapped reads, total number/proportion of mapped non-duplicate reads, and number/proportion of reads with mapping quality greater than 20

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")
QCmetric_raw = get_samp_QC(bambedObj)

SCOPE documentation built on Nov. 8, 2020, 5:27 p.m.