CreateSamplesFas: CreateSamplesFas() function

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

CreateSamplesFas() function

Description

CreateSamplesFas creates a set of FASTA files with the sequences present in each sample in a 'dada2' sequence table.

Usage

CreateSamplesFas(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 set of FASTA files with the sequences present in each sample in the sequence table.The sequences are named in the FASTA files by an index number corresponding to their column number in the sequence table, thus identical sequences will have identical sample names in all the FASTA files.

See Also

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

Examples

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

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