setUp: Setup repseq object for differential abudance analysis, CDR3...

View source: R/RepDaAnalysisFns.R

setUpR Documentation

Setup repseq object for differential abudance analysis, CDR3 counts are changed to counts per million for all samples

Description

Setup repseq object for differential abudance analysis, CDR3 counts are changed to counts per million for all samples

Usage

setUp(sampleNames = NULL, samGroup = NULL, normToCPM = T)

Arguments

sampleNames

is a vector of sample names (that have been already read into R )

samGroup

a vector of group labels, e.g c(0,0,1,1), 0 for samples in first condition and 1 for samples in second condition.

normToCPM

normalize all repseq samples to a total repertoire size of 1e6 (1 million) by default.

Value

a repSeq object which is a list containing the raw data (normalized to 1e6 in all samples if normToCPM is set to true),the sample names, and their group status


dyohanne/RepAn documentation built on Feb. 3, 2023, 2:41 p.m.