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)A character(1) specifying the path to the tab-separated
(TSV) file created manually using megadepth_shell() or on a previous
get_coverage() run.
A logical(1) controlling whether to suppress messages when
reading the data.
A GRanges-class object with the coverage summarization across the annotation ranges.
A tibble::tibble() 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()
#> The latest megadepth version is 1.2.0
#> This is not an interactive session, therefore megadepth has been installed temporarily to
#> /tmp/RtmpmgolT5/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
#> GRanges object with 4 ranges and 1 metadata column:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr10 0-10 * | 0.00
#> [2] chr10 8756697-8756762 * | 15.85
#> [3] chr10 4359156-4359188 * | 3.00
#> [4] GL000219.1 168500-168620 * | 1.26
#> -------
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
## 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)
#> RleList of length 2
#> $chr10
#> integer-Rle of length 8756762 with 5 runs
#> Lengths: 10 4359145 33 4397508 66
#> Values : 1 0 1 0 1
#>
#> $GL000219.1
#> integer-Rle of length 168620 with 2 runs
#> Lengths: 168499 121
#> Values : 0 1
#>
## The coverage data can also be read as a `tibble::tibble()`
read_coverage_table(tsv_file)
#> # A tibble: 4 × 4
#> chr start end score
#> <chr> <int> <int> <dbl>
#> 1 chr10 0 10 0
#> 2 chr10 8756697 8756762 15.8
#> 3 chr10 4359156 4359188 3
#> 4 GL000219.1 168500 168620 1.26