splitBam {ATACseqQC} | R Documentation

## prepare bam files for downstream analysis

### Description

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

### Usage

    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

    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")
    }

[Package ATACseqQC version 1.11.8 Index]