getSamplePairIDs: SampleIDs for Paired End Datasets

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

SampleIDs for Paired End Datasets

Description

Utilities to map between paired end specific files and their parent SampleID.

Usage

getSamplePairIDs(sampleID, annotationFile = "Annotation.txt")

originalSamplePairID(sampleID, annotationFile = "Annotation.txt")

Arguments

sampleID	a SampleID, that may or may not have a paired end suffix (e.g. "_1", "_2")
annotationFile	the sample annotation file containing the details about this sample

Details

With paired end data, there are some pipeline tools that operate on each paired end file half separately. These need the pair suffix present. Most other tools just want the 'parent' SampleID with no suffix. These utilities map back and forth between those two formats.

Value

For getSamplePairIDs(), a vector of at most length 2, with pair specific SampleIDs for this sample. If the dataset is not paired end data, the given SampleID is returned as is.

For originalSamplePairID, a single SampleID with any pair suffix removed.

robertdouglasmorrison/DuffyTools documentation built on April 13, 2025, 8:51 p.m.