prepare bam files for downstream analysis

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)
)

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

See also

shiftGAlignmentsList, splitGAlignmentsByCut, and writeListOfGAlignments

Author

Jianhong Ou

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")
}