TSSQC {esATAC} | R Documentation

## Quality control for transcription start site(TSS) reads enrichment

### Description

These functions are used to generate the reads coverage plot around TSS.

### Usage

    atacTSSQC(
      atacProc,
      txdbKnownGene = NULL,
      bsgenome = NULL,
      reportPrefix = NULL,
      bedInput = NULL,
      fragLenRange = c(0, 2000),
      tssUpdownstream = 1000,
      newStepType = "TSSQC",
      ...
    )

    ## S4 method for signature 'ATACProc'
    atacTSSQC(
      atacProc,
      txdbKnownGene = NULL,
      bsgenome = NULL,
      reportPrefix = NULL,
      bedInput = NULL,
      fragLenRange = c(0, 2000),
      tssUpdownstream = 1000,
      newStepType = "TSSQC",
      ...
    )

    tssQC(
      bedInput,
      txdbKnownGene = NULL,
      bsgenome = NULL,
      reportPrefix = NULL,
      fragLenRange = c(0, 2000),
      tssUpdownstream = 1000,
      newStepType = "TSSQC",
      ...
    )

### Arguments

`atacProc` | `ATACProc-class` object scalar. It has to be the return value of upstream process: `atacSamToBed`, `atacBedUtils`.
`txdbKnownGene` | `TxDb` object scalar. TxDb object for specific species.
`bsgenome` | `BSGenome` object scalar. BSGenome object for specific species.
`reportPrefix` | `Character` scalar. The prefix of report files path.
`bedInput` | `Character` scalar. BED file input path.
`fragLenRange` | `Interger` vector of 2 element. The fragment length ranges.
`tssUpdownstream` | `Interger` scalar. The upstream and downstrem from TSS locations.
`newStepType` | `Character` scalar. New class name
`...` | 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, `atacProc` should be set `NULL` or you can use `tssQC` instead.

### Value

An invisible `ATACProc-class` object scalar for downstream analysis.

### Author(s)

Zheng Wei

### See Also

`atacSamToBed` `samToBed` `atacBedUtils` `bedUtils`

### Examples

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

    bedbzfile <- system.file(package="esATAC", "extdata", "chr20.50000.bed.bz2")
    bedfile <- file.path(td,"chr20.50000.bed")
    bunzip2(bedbzfile,destname=bedfile,overwrite=TRUE,remove=FALSE)
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    library(BSgenome.Hsapiens.UCSC.hg19)
    tssQC(bedfile,TxDb.Hsapiens.UCSC.hg19.knownGene,BSgenome.Hsapiens.UCSC.hg19,fragLenRange=c(180,247))

    dir(td)

[Package esATAC version 1.12.0 Index]