alignmentFeatureStatistics {ORFik} | R Documentation

## Create alignment feature statistcs

### Description

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.

### Usage

    alignmentFeatureStatistics(df, type = "ofst", BPPARAM = bpparam())

### Arguments

`df` | an ORFik `experiment`
`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 `bpparam()$workers`. You can also add a time remaining bar, for a more detailed pipeline.

### Value

a data.table of the statistcs

[Package ORFik version 1.12.13 Index]