bed.genomecov¶
compute genomewide feature coverage
description¶
bed.genomecov is a wrapper script for ‘bedtools genomecov’, which computes genomewide coverage of genomic intervals, such as aligned reads.
usage¶
bed.genomecov( intervalfile, genomefile , covmode = "-bg" , scalar = "rpm", bam = FALSE )
arguments¶
| Main options | Description |
|---|---|
| intervalfile | character vector of length 1 specifying the path to the interval file name to calculate genome coverage of. By default, a bed file is expected, unless bam=TRUE. |
| genomefile | character vector of length 1 specifying the path to genome file specifying the chromosome sizes of the genome. |
| covmode | character vector of length 1 specifying the output format. Default is “-bg”. See details. |
| scalar | number to multiply coverage by. Default is “rpm”, which multiplies the coverage to report intervals per million. |
| bam | a logical value indicating if the input interval file is a bam file. default is FALSE (input is a bed file) |
output¶
bed.genomecov will output a bedGraph file of the coverage of intervals at each base pair in the entire genome. By default (covmode = “-bg”), contiguous regions with the same coverage will be collapsed into the same bedGraph interval.
examples¶
calculate genomewide coverage in reads per million of intervals in a bed file¶
> bed.genomecov ( "H3K36me3-reads.bed" , genomefile = "/path/to/genomefile" )
[1] "H3K36me3-reads.bg"
calculate genomewide coverage of intervals in a bed file reporting absolute coverage¶
> bed.genomecov ( "H3K36me3-reads.bed" , genomefile = "/path/to/genomefile" , scalar = 1 )
calculate genomewide coverage of intervals in a bam file¶
> bed.genomecov ( "H3K36me3-reads.bam" , genomefile = "/path/to/genomefile" , bam = TRUE )