exportFasta: Export sequences in fasta format

In LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description

Export nucleotide or amino acid sequences in fasta format.

Usage

exportFasta(list, type = "nucleotide", names = c("rank", "aminoAcid",
  "count"))

Arguments

list	A list of data frames consisting of antigen receptor sequences imported by the LymphoSeq function readImmunoSeq.
type	A character vector indicating whether "aminoAcid" or "nucleotide" sequences should be exported. If "aminoAcid" 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.

Value

Exports fasta files to the working directory.

Examples

file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path)

exportFasta(list = file.list, type = "nucleotide", names = c("rank", "aminoAcid", "count"))

productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")

exportFasta(list = productive.aa, type = "aminoAcid", names = "frequencyCount")

LymphoSeq documentation built on Nov. 8, 2020, 8:09 p.m.