read_coverage {megadepth} | R Documentation |
Read an *annotation.tsv
file created by get_coverage()
or manually by
the user using Megadepth.
read_coverage(tsv_file, verbose = TRUE) read_coverage_table(tsv_file)
tsv_file |
A |
verbose |
A |
A GRanges-class object with the coverage summarization across the annotation ranges.
A tibble::tible()
with columns chr
, start
, end
and score
.
read_coverage_table
: Read a coverage TSV file created by Megadepth as
a table
Other Coverage functions:
get_coverage()
## Install if necessary install_megadepth() ## Locate example BigWig and annotation files example_bw <- system.file("tests", "test.bam.all.bw", package = "megadepth", mustWork = TRUE ) annotation_file <- system.file("tests", "testbw2.bed", package = "megadepth", mustWork = TRUE ) ## Compute the coverage bw_cov <- get_coverage(example_bw, op = "mean", annotation = annotation_file) bw_cov ## Read in the coverage file again, using read_coverage() ## First, lets locate the tsv file that was generated by get_coverage() tsv_file <- file.path(tempdir(), "bw.mean.annotation.tsv") bw_cov_manual <- read_coverage(tsv_file) stopifnot(identical(bw_cov, bw_cov_manual)) ## To get an RleList object, just like the one you would get ## from using rtracklayer::import.bw(as = "RleList") directly on the ## BigWig file, use: GenomicRanges::coverage(bw_cov_manual) ## The coverage data can also be read as a `tibble::tibble()` read_coverage_table(tsv_file)