CreateFas: CreateFas() function

In MHCtools: Analysis of MHC Data in Non-Model Species

CreateFas() function

Description

CreateFas creates a FASTA file with all the sequences in a 'dada2' sequence table.

Usage

CreateFas(seq_table, path_out)

Arguments

seq_table	seq_table is a sequence table as output by the 'dada2' pipeline, which has samples in rows and nucleotide sequence variants in columns.
path_out	is a user defined path to the folder where the output files will be saved.

Details

If you publish data or results produced with MHCtools, please cite both of the following references: Roved, J. (2022). MHCtools: Analysis of MHC data in non-model species. Cran. Roved, J. (2024). MHCtools 1.5: Analysis of MHC sequencing data in R. In S. Boegel (Ed.), HLA Typing: Methods and Protocols (2nd ed., pp. 275–295). Humana Press. https://doi.org/10.1007/978-1-0716-3874-3_18

Value

A FASTA file with all the sequences in a 'dada2' sequence table. The sequences are named in the FASTA file by an index number corresponding to their column number in the sequence table.

See Also

CreateSamplesFas; for more information about 'dada2' visit <https://benjjneb.github.io/dada2/>

Examples

seq_table <- sequence_table_fas
path_out <- tempdir()
CreateFas(seq_table, path_out)

MHCtools documentation built on April 3, 2025, 7:17 p.m.