splitBam: prepare bam files for downstream analysis

Description Usage Arguments Value Author(s) See Also Examples

View source: R/splitBam.R

Description

shift the bam files by 5'ends and split the bam files.

Usage

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splitBam(
  bamfile,
  tags,
  index = bamfile,
  outPath = NULL,
  txs,
  genome,
  conservation,
  positive = 4L,
  negative = 5L,
  breaks = c(0, 100, 180, 247, 315, 473, 558, 615, Inf),
  labels = c("NucleosomeFree", "inter1", "mononucleosome", "inter2", "dinucleosome",
    "inter3", "trinucleosome", "others"),
  seqlev = paste0("chr", c(1:22, "X", "Y")),
  cutoff = 0.8,
  flag = scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery = FALSE,
    isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE)
)

Arguments

bamfile

character(1). File name of bam.

tags

A vector of characters indicates the tags in bam file.

index

The names of the index file of the 'BAM' file being processed; This is given without the '.bai' extension.

outPath

Output file path.

txs

GRanges of transcripts.

genome

An object of BSgenome

conservation

An object of GScores.

positive

integer(1). the size to be shift for positive strand

negative

integer(1). the size to be shift for negative strand

breaks

A numeric vector for fragment size of nucleosome free, mononucleosome, dinucleosome and trinucleosome

labels

A vector of characters indicates the labels for the levels of the resulting category. The length of labels = length of breaks - 1

seqlev

A vector of characters indicates the sequence levels.

cutoff

numeric(1). Cutoff value for prediction by randomForest.

flag

An integer(2) vector used to filter reads based on their 'flag' entry.

Value

an invisible list of GAlignments

Author(s)

Jianhong Ou

See Also

shiftGAlignmentsList, splitGAlignmentsByCut, and writeListOfGAlignments

Examples

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if(Sys.getenv("USER")=="jianhongou"){
bamfile <- system.file("extdata", "GL1.bam", package="ATACseqQC")
tags <- c("AS", "XN", "XM", "XO", "XG", "NM", "MD", "YS", "YT")
library(BSgenome.Hsapiens.UCSC.hg19)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txs <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(phastCons100way.UCSC.hg19)
objs <- splitBam(bamfile, tags,
                 txs=txs, genome=Hsapiens,
                 conservation=phastCons100way.UCSC.hg19,
                 seqlev="chr1")
}

jianhong/ATACseqQC documentation built on Feb. 16, 2020, 7:07 p.m.