featureCounts2se: Create a SummarizedExperiment object from featureCounts...

In almeidasilvaf/bear: Building Expression Atlas from RNA-Seq data

Create a SummarizedExperiment object from featureCounts output

Description

Create a SummarizedExperiment object from featureCounts output

Usage

featureCounts2se(sample_info = NULL, fc_output = NULL)

Arguments

sample_info	Data frame of sample metadata created with the functions create_sample_info.
fc_output	Either a gene expression matrix generated by fcount, or the path to the .tsv file containing the gene expression matrix as generated by fcount.

Value

A SummarizedExperiment object.

Examples

data(sample_info)
mappingdir <- system.file("extdata", package="bears")
gff_path <- system.file("extdata", "Homo_sapiens.GRCh37.75_subset.gtf",
                        package="bears")
fcountsdir <- file.path(tempdir(), "fcountsdir")
if(subread_is_installed()) {
    counts <- featureCounts(sample_info, mappingdir, gff_path, fcountsdir)
    se <- featureCounts2se(sample_info, counts)
}

almeidasilvaf/bear documentation built on April 14, 2023, 7:03 p.m.