| splitBam {ATACseqQC} | R Documentation |
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")