splitBam: prepare bam files for downstream analysis
In ATACseqQC: ATAC-seq Quality Control

Description Usage Arguments Value Author(s) See Also Examples

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

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)
)

`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.

an invisible list of GAlignments

Jianhong Ou

shiftGAlignmentsList, splitGAlignmentsByCut, and writeListOfGAlignments

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")
}