GetGatkPipelineTabs: GetGatkPipelineTabs

In gimelbrantlab/Qllelic: Detects differential allelic imbalance from RNA-seq data

GetGatkPipelineTabs

Description

Loads the working parts of tables ("ID", allele count 2x columns, "contig" if specified); concatenates (uniting merge) tables from all provided files.

Usage

GetGatkPipelineTabs(inFiles, nReps, contigs = vector())

Arguments

inFiles	A vector of full pathes to files with alelleic counts tables; necessary columns: "ID", pairs of ref and alt allelic counts; optionally, for filtering, "contig"
nReps	A vector of numbers, either: (1) each entry is a number of replicates in the corresponding file; (2) for one file only, each entry is a number of replicates corresponding to particular experiment
contigs	Optional (default=vector()), parameter defining if the resulting table should be filtered by contig column (preserving only rows corresponding to a given vector), default set to empty vector() and no filtering applied

Value

A concatenated table with allele counts for all replicates, each row corresponds to a feature ("ID")

gimelbrantlab/Qllelic documentation built on Dec. 30, 2024, 4:02 p.m.