LibComplexQC {esATAC} | R Documentation

## Quality control for library complexity

### 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)

[Package esATAC version 1.12.0 Index]