Description Usage Arguments Value Examples
Export nucleotide or amino acid sequences in fasta format.
1 2 | exportFasta(list, type = "nucleotide", names = c("rank", "aminoAcid",
"count"))
|
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. |
Exports fasta files to the working directory.
1 2 3 4 5 6 7 8 9 | 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")
|
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