brainflowprobes_cov: Extract coverage data for a set of regions

In LieberInstitute/brainflowprobes: Plots and annotation for choosing BrainFlow target probe sequence

Extract coverage data for a set of regions

Description

This function extracts the data from the BigWig coverage files that is then used by four_panels. This function can take a while to run depending on your internet connection. Furthermore, this function relies on functionality in the rtracklayer package for reading BigWig files which does not work in Windows machines. The data extracted by this function is also used by plot_coverage.

Usage

brainflowprobes_cov(REGION, PD = brainflowprobes::pd, VERBOSE = TRUE)

Arguments

REGION	Either a single hg19 genomic sequence including the chromosome, start, end, and optionally strand separated by colons (e.g., 'chr20:10199446-10288068:+'), or a string of sequences. Must be character. Chromosome must be proceeded by 'chr'.
PD	A list of data.frames with the sumMapped and files columns. Defaults to the data included in this package.
VERBOSE	A logical value indicating whether to print updates from the process of loading the data from the BigWig files.

Value

A list of region coverage coverage data.frame lists used by four_panels and plot_coverage. That is, a list with one element per dataset in pd (so four: Sep, Deg, Cell, Sort). Each element of the output list is a list with one data.frame per input region. In the case of four_panels_example_cov there was only one input region hence each region coverage data.frame list has one element. A region coverage data.frame has one column per sample and one row per genome base-pair for the given region and dataset.

Author(s)

Leonardo Collado-Torres

Examples

## This function loads data from BigWig files using the rtracklayer package.
## This functionality is not supported on Windows OS machines!
if (.Platform$OS.type != "windows") {
    ## How long this takes to run will depend on your internet connection.
    example_cov <- brainflowprobes_cov("chr20:10286777-10288069:+",
        PD = lapply(brainflowprobes::pd, head, n = 2)
    )

    ## Output examination:
    # A list with one element per element in brainflowprobes::pd
    stopifnot(is.list(example_cov))
    stopifnot(identical(
        names(example_cov),
        names(brainflowprobes::pd)
    ))

    # For each dataset, brainflowprobes_cov() returns a list of region
    # coverage data.frames. In this example, there was a single input region.
    stopifnot(all(
        sapply(example_cov, length) ==
            length(
                GenomicRanges::GRanges("chr20:10286777-10288069:+")
            )
    ))

    # Then each data.frame itself has 1 row per genome base-pair in the region
    stopifnot(
        all(
            sapply(example_cov, function(x) {
                nrow(x[[1]])
            }) ==
                GenomicRanges::width(
                    GenomicRanges::GRanges("chr20:10286777-10288069:+")
                )
        )
    )

    # and one column per sample in the dataset unless you subsetted the data
    # like we did earlier when creating "example_cov".
    stopifnot(identical(
        sapply(four_panels_example_cov, function(x) {
            ncol(x[[1]])
        }),
        sapply(pd, nrow)
    ))
}

## This is how the example data included in the package was made:
## Not run: 
## This can take about 10 minutes to run!
four_panels_example_cov <- brainflowprobes_cov("chr20:10286777-10288069:+")

## End(Not run)


## If you are interested, you could download all the BigWig files
## in the \code{brainflowprobes::pd} list of data.frames from the
## \code{files} column to your disk. Doing so will greatly increase the
## speed for \code{brainflowprobes_cov} and the functions that depend on
## this data. Then edit \code{brainflowprobes::pd} \code{files} to point to
## your local files.

## Web location of BigWig files
lapply(brainflowprobes::pd, function(x) head(x$files))

LieberInstitute/brainflowprobes documentation built on May 6, 2024, 5:55 a.m.