CreateFas {MHCtools}

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., Hansson, B., Stervander, M., Hasselquist, D., & Westerdahl, H. 2022. MHCtools - an R package for MHC high-throughput sequencing data: genotyping, haplotype and supertype inference, and downstream genetic analyses in non-model organisms. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13645

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)