bedtoolsMulticov: Calculate coverage of multiple bams files over intervals in a...
In dvera/gyro: gyro: Genomic utility wrappers in R

bedtools.multicov is a wrapper for bedtools multicov.

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bedtoolsMulticov(bamFiles, bedfile, outname, split = FALSE,
  samestrand = FALSE, diffstrand = FALSE, q = 10, duplicates = FALSE,
  onlyPaired = FALSE)

`bamFiles`	A character vector of paths to bam files.
`bedfile`	A string specifying the path to the bed file within which to calculate coverage of bams.
`outname`	A character vector of length one specifying the concatenated file name.
`split`	Boolean. If TRUE, “split” BAMs or BED12 entries will be treated as distinct BED intervals.
`samestrand`	Boolean. If TRUE, same strandedness is required for a read to be counted. That is, only report hits in B that overlap A on the same strand. If FALSE, overlaps are reported without respect to strand. Conflicts with diffstrand.
`diffstrand`	Boolean. If TRUE, different strandedness is required for a read to be counted. That is, only report hits in B that overlap A on the opposite strand. If FALSE, overlaps are reported without respect to strand. Conflicts with samestrand.
`q`	A positive integer specifying the minimum quality of a read for it to be counted.
`duplicates`	Boolean. If TRUE, include duplicate reads. Default (FALSE) counts non-duplicates only.
`onlyPaired.`	Boolean. If TRUE, only properly-paired reads will be counted. Default counts all alignments with MAPQ > q, regardless of the BAM FLAG field.