BAM2GenomicRanges {Repitools} | R Documentation |
A wrapper script for coverting the contents of BAM files for use with
GenomicRanges
classes.
## S4 method for signature 'character' BAM2GRanges(path, what = character(), flag = scanBamFlag(isUnmappedQuery = FALSE, isDuplicate = FALSE), verbose = TRUE) ## S4 method for signature 'character' BAM2GRangesList(paths, what = character(), flag = scanBamFlag(isUnmappedQuery = FALSE, isDuplicate = FALSE), verbose = TRUE)
path |
A character vector of length 1. The path of the BAM file. |
paths |
A character vector of possibly any length. The paths of the BAM files. |
what |
What optional attributes of a read to retain. See
|
flag |
What kinds of reads to retain. See
|
verbose |
Whether to print the progess of processing. |
For the single pathname method; a GRanges object. For the multiple pathnames method; a GRangesList object.
Dario Strbenac
tiny.BAM <- system.file("extdata", "ex1.bam", package = "Rsamtools") if(length(tiny.BAM) > 0) print(BAM2GRanges(tiny.BAM))