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
andinfer_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)
}