bam_to_bigwig {megadepth} | R Documentation |
Given an input BAM file, convert this to the BigWig format which can then be
used in get_coverage()
.
bam_to_bigwig( bam_file, prefix = file.path(tempdir(), basename(bam_file)), min_unique_qual = FALSE, double_count = FALSE, overwrite = FALSE )
bam_file |
A |
prefix |
A |
min_unique_qual |
A |
double_count |
A |
overwrite |
A |
Note that this functionality is currently not supported on Windows by Megadepth.
A character()
with the path to the output files(s).
## Install the latest version if necessary install_megadepth(force = TRUE) ## Find the example BAM file example_bam <- system.file("tests", "test.bam", package = "megadepth", mustWork = TRUE ) ## Create the BigWig file ## Currently Megadepth does not support this on Windows if (!xfun::is_windows()) { example_bw <- bam_to_bigwig(example_bam, overwrite = TRUE) ## Path to the output file(s) generated by bam_to_bigwig() example_bw ## Use the all.bw file in get_coverage(), first find an annotation file annotation_file <- system.file("tests", "testbw2.bed", package = "megadepth", mustWork = TRUE ) ## Compute the coverage bw_cov <- get_coverage( example_bw["all.bw"], op = "mean", annotation = annotation_file ) bw_cov }