alignmentFeatureStatistics {ORFik} | R Documentation |
Among others how much reads are in mRNA, introns, intergenic, and check of reads from rRNA and other ncRNAs. The better the annotation / gtf used, the more results you get.
alignmentFeatureStatistics(df, type = "ofst", BPPARAM = bpparam())
df |
an ORFik |
type |
a character(default: "default"), load files in experiment or some precomputed variant, either "ofst", "bedo", "bedoc" or "pshifted". These are made with ORFik:::convertLibs() or shiftFootprintsByExperiment(). Can also be custom user made folders inside the experiments bam folder. It acts in a recursive manner with priority: If you state "pshifted", but it does not exist, it checks "ofst". If no .ofst files, it uses "default", which always exists. |
BPPARAM |
how many cores/threads to use? default: bpparam().
To see number of threads used, do |
a data.table of the statistcs