read_coverage: Read a coverage TSV file created by Megadepth
In megadepth: megadepth: BigWig and BAM related utilities

Description Usage Arguments Value Functions See Also Examples

View source: R/read_coverage.R

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

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read_coverage(tsv_file, verbose = TRUE)

read_coverage_table(tsv_file)

`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.

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)