Infer library strandedness
Usage
infer_strandedness(
mapping_passed = NULL,
bedpath = NULL,
mappingdir = "results/04_read_mapping",
sample_n = 4e+05
)
Arguments
- mapping_passed
Metadata of samples that passed mapping QC. This can be obtained with
mapping_pass
.- bedpath
Path to BED file. GFF files can be converted to BED with
gff2bed
.- mappingdir
Directory where .bam files are stored.
- sample_n
Numeric indicating the number of reads to sample from .bam file to infer strandedness. Default: 400000.
Value
A data frame with sample metadata as in mapping_passed, but with an additional column named 'Orientation' containing library strandedness for each BioProject.
Examples
data(sample_info)
mapping_passed <- sample_info[, -grep("Orientation", names(sample_info))]
bedpath <- system.file("extdata", "Homo_sapiens.GRCh37.75_subset.bed",
package="bears")
mappingdir <- system.file("extdata", package = "bears")
if(rseqc_is_installed()) {
s <- infer_strandedness(mapping_passed, bedpath, mappingdir)
}