splitBam: prepare bam files for downstream analysis
In jaime11/Transcription-Factor-Footprinting: 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, 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)

`bamfile`	character(1). File name of bam.
`tags`	A vector of characters indicates the tags in bam file.
`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 freee, 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.

an invisible list of GAlignments

Jianhong Ou

shiftGAlignmentsList, splitGAlignmentsByCut, and writeListOfGAlignments

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")