assembleFastaDb: assembleFastaDb

In heuselm/igseqr: Integrate MiXCR BCR/IG-Seq and DIA-MS data to profile immune repertoire evolution

assembleFastaDb

Description

assemble fasta database of variable domains from MiXCR IgSeq results

Usage

assembleFastaDb(
  IGSeq_resultset,
  dataset_tag = NULL,
  write_fasta = TRUE,
  write_fasta_per_sample = FALSE,
  write_clone_tables = TRUE,
  write_fasta_subset_cloneIdGlobal = NULL,
  gsub_sample_id = NULL,
  prefix_chain_type = FALSE
)

Arguments

IGSeq_resultset	IgSeq resultset imported by importIgSeq function.
dataset_tag	Dataset tag introduced to cloneIdGlobal and output files. Default: Input IGSeq R object name
write_fasta	Whether to write .fasta files to working directory. Default: TRUE
write_fasta_per_sample	Whether to write separate .fasta files per sample. Default: FALSE
write_clone_tables	Whether to write clone .tsv tables next to .fasta files. Default: TRUE
gsub_sample_id	character vector of length 2, Whether to replace certain string in sample IDs (element 1) with (element 2). Default: Null (no editing of SAMPLE_ID)
prefix_chain_type	whether chain_type should be prepended to(at the beginning of) cloneIdGlobal. Default: FALSE Default: Null, All clones included.
subset_cloneIdGlobal	Whether to subset clones to be included in fasta file. Character vector of global clone IDs.

Value

IGSeq_resultset with added element step6_clonestofasta

heuselm/igseqr documentation built on March 19, 2022, 7:28 p.m.