LibComplexQC: Quality control for library complexity

In esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis

Description

The function calculate the nonredundant fraction of reads (NRF). Its definition is number of distinct uniquely mapping reads (i.e. after removing duplicates) / Total number of reads. The function also Calculate PCR Bottlenecking Coefficient 1 (PBC1) and PCR Bottlenecking Coefficient 2 (PBC2). PBC1=M1/M_DISTINCT and PBC2=M1/M2, where M1: number of genomic locations where exactly one read maps uniquely, M2: number of genomic locations where two reads map uniquely M_DISTINCT: number of distinct genomic locations to which some read maps uniquely.

Usage

atacLibComplexQC(
  atacProc,
  reportOutput = NULL,
  samInput = NULL,
  singleEnd = FALSE,
  subsampleSize = Inf,
  ...
)

## S4 method for signature 'ATACProc'
atacLibComplexQC(
  atacProc,
  reportOutput = NULL,
  samInput = NULL,
  singleEnd = FALSE,
  subsampleSize = Inf,
  ...
)

libComplexQC(
  samInput,
  reportOutput = NULL,
  singleEnd = FALSE,
  subsampleSize = Inf,
  ...
)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: atacBowtie2Mapping bowtie2Mapping
reportOutput	Character scalar. The report file path
samInput	Character scalar. The SAM file input path.
singleEnd	Character scalar. Single end data if TRUE. Paired end data if FALSE.
subsampleSize	Integer scalar. Down sample reads if the number is less than total number when subsample is TRUE
...	Additional arguments, currently unused.

Details

The parameter related to input and output file path will be automatically obtained from ATACProc-class object(atacProc) or generated based on known parameters if their values are default(e.g. NULL). Otherwise, the generated values will be overwrited. If you want to use this function independently, you can use libComplexQC instead.

Value

An invisible libComplexQC object scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

atacBowtie2Mapping bowtie2Mapping

Examples

library(R.utils)
td <- tempdir()
setTmpDir(td)

sambzfile <- system.file(package="esATAC", "extdata", "Example.sam.bz2")
samfile <- file.path(td,"Example.sam")
bunzip2(sambzfile,destname=samfile,overwrite=TRUE,remove=FALSE)
atacproc<-libComplexQC(samInput = samfile)

esATAC documentation built on Nov. 8, 2020, 6:58 p.m.