get_count_matrix {ODER} | R Documentation

## Generate the count matrix

### Description

Scores the mean coverage of the expressed regions as a count matrix

### Usage

    get_count_matrix(bw_paths, annot_ers, cols = NULL)

### Arguments

`bw_paths` | Vector containing the bigwig file paths to read in
`annot_ers` | GRangesList containing the annotated ERs (product of `annotatERs`)
`cols` | A dataframe containing the information to be used as colData for the output. If NULL then the bw_paths will be used for the colData

### Value

A Ranged Summarized Experiment containing the gene counts as an assay

### Examples

    megadepth::install_megadepth()

    rec_url <- recount::download_study(
        project = "SRP012682",
        type = "samples",
        download = FALSE
    )
    # file_cache is an internal function to download a bigwig file from a link
    # if the file has been downloaded recently, it will be retrieved from a cache
    bw_path <- file_cache(rec_url[1])

    ex_opt_ers <- GenomicRanges::GRanges(
        seqnames = S4Vectors::Rle(c("chr1", "chr2"), c(4, 1)),
        ranges = IRanges::IRanges(
            start = c(1:5),
            end = seq(100, 500, 100)
        )
    )

    example_cm <- get_count_matrix(
        bw_paths = c(bw_path, bw_path),
        annot_ers = ex_opt_ers
    )
    example_cm

[Package ODER version 1.0.0 Index]