featureCounts: Count reads with featureCounts

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

Count reads with featureCounts

Description

Count reads with featureCounts

Usage

featureCounts(
  sample_info = NULL,
  mappingdir = "results/04_read_mapping",
  gff_path = NULL,
  fcountsdir = "results/05_quantification/featureCounts",
  threads = 2
)

Arguments

sample_info	Data frame of sample metadata created with the functions create_sample_info and infer_strandedness.
mappingdir	Directory where .bam files are stored.
gff_path	Path to GFF/GTF file with annotations.
fcountsdir	Directory where the matrix of gene-level read counts will be stored.
threads	Number of threads for featureCounts. Default: 2.

Value

A gene expression matrix with genes in row names and samples in column names. Two .tsv files with the gene expression matrix and count stats are saved to fcountsdir.

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)
}

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