exportFasta {LymphoSeq} | R Documentation

## Export sequences in fasta format

### 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")

[Package LymphoSeq version 1.14.0 Index]