QC_count_tables: Create count table info for QC report

In ORFik: Open Reading Frames in Genomics

Description

The better the annotation / gtf used, the more results you get.

Usage

QC_count_tables(df, out.dir, type = "ofst", BPPARAM = bpparam())

Arguments

df	an ORFik experiment
out.dir	optional output directory, default: dirname(df$filepath[1]). Will make a folder called "QC_STATS" with all results in this directory.
type	a character(default: "default"), load files in experiment or some precomputed variant, either "ofst", "bedo", "bedoc" or "pshifted". These are made with ORFik:::convertLibs() or shiftFootprintsByExperiment(). Can also be custom user made folders inside the experiments bam folder.
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers

Value

a data.table of the count info

ORFik documentation built on March 27, 2021, 6 p.m.