createDecoyCDR3s_V2: Create decoy CDR3 sequences and add to each repertoire sample

In dyohanne/RepAn: Differential abundance Analysis for deep sequenced immune repertoire (Repseq) datasets

Create decoy CDR3 sequences and add to each repertoire sample

Description

Function creates decoy CDR3 sequences either by random sampling from a reference repertoire or by in-silico generation per each sample

Usage

createDecoyCDR3s_V2(repSeqObj, seqType = c("NT", "AA"),
  decoyProp = 0.5, randromSelect = T, paired = T,
  referenceSetFileInRDS = NULL)

Arguments

repSeqObj	is an object containing all repertoire sample data
seqType	subsequence type to consider, either NT (nucleotide) or AA (amino acid).
decoyProp	the proportion of decoy CDR3s to include in each sample (this proportion is in comparison to the resampled repertoire size for each sample). Default is 0.5.
randromSelect	Boolean; should the decoy CDR3s be randomly sampled from reference or in-silico generated. Default is random sampling from the reference.
paired	Boolean; whether samples are matched/paired.If true, and randromSelect is true, random selection of decoys for the matched samples is done from a random subset of CDR3s from the total reference.
referenceSetFileInRDS	Reference TCR CDR3 repertoire (in immunoseq format and in RDS file type) to use as a reference set. If not provided, the reference dataset would be used that comes with the package would be used.

Value

repSeq data Object containing repertoire samples that contain decoy CDR3 sequences

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