TSSQC: Quality control for transcription start site(TSS) reads...

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

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)

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.