exportFasta: Export sequences in fasta format

In elulu3/LymphoSeqTest: Analyze high-throughput sequencing of T and B cell receptors

Export sequences in fasta format

Description

Export junction or amino acid sequences in fasta format.

Usage

exportFasta(
  study_table,
  type = "junction",
  names = c("rank", "junction_aa", "duplicate_count")
)

Arguments

type	A character vector indicating whether "junction_aa" or "junction" sequences should be exported. If "junction_aa" is specified, then run productiveSeqs first.
names	A character vector of one or more column names to name the sequences. If "rank" is specified, then the rank order of the sequences by frequency is used.
sample_table	A tibble consisting of antigen receptor sequences imported by the LymphoSeq function readImmunoSeq.

Value

Exports fasta files to the working directory.

Examples

file_path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq2")

stable <- readImmunoSeq(path = file_path)

exportFasta(study_table = stable, type = "junction", names = c("junction_aa", "duplicate_count"))

atable <- productiveSeq(study_table = stable, aggregate = "junction_aa")

exportFasta(study_table = atable, type = "junction_aa", names = "duplicate_frequency")

elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.