bam_to_bigwig: Convert a BAM file to a BigWig
In megadepth: megadepth: BigWig and BAM related utilities

Description Usage Arguments Details Value Examples

View source: R/bam_to_bigwig.R

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 `character(1)` with the path to the input BAM file.
`prefix`	A `character(1)` specifying the output file prefix. This function creates a BigWig file called `{prefix}.all.bw`. By default, the prefix is the BAM file name and the file is created in the `tempdir()` and will be deleted after you close your R session.
`min_unique_qual`	A `integer(1)` specifying a mapping quality threshold and only bases above this will be used to generate the BigWig. If set to `FALSE` this argument is not used by Megadepth. Otherwise it will generate files `{prefix}.unique.bw` and `{prefix}.unique.tsv`.
`double_count`	A `logical(1)` determining whether to count the overlapping ends of paired ends reads twice.
`overwrite`	A `logical(1)` specifying whether to overwrite the output file(s), if they exist already.

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
}