read_coverage: Read a coverage TSV file created by Megadepth

In LieberInstitute/megadepth: megadepth: BigWig and BAM related utilities

Read a coverage TSV file created by Megadepth

Description

Read an ⁠*annotation.tsv⁠ file created by get_coverage() or manually by the user using Megadepth.

Usage

read_coverage(tsv_file, verbose = TRUE)

read_coverage_table(tsv_file)

Arguments

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.
verbose	A logical(1) controlling whether to suppress messages when reading the data.

Value

A GRanges-class object with the coverage summarization across the annotation ranges.

A tibble::tibble() with columns chr, start, end and score.

Functions

• read_coverage_table(): Read a coverage TSV file created by Megadepth as a table

See Also

Other Coverage functions: get_coverage()

Examples

## 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)

LieberInstitute/megadepth documentation built on May 6, 2024, 7:12 p.m.