QC_count_tables {ORFik}R Documentation

Create count table info for QC report

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. Warning: If you assign not default path, you will have a hazzle to load files later. Much easier to load count tables, statistics, ++ later with default.

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 count info


[Package ORFik version 1.12.13 Index]