CreateHpltOccTable: CreateHpltOccTable() function

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

CreateHpltOccTable() function

Description

CreateHpltOccTable is designed to create a haplotype-sequence occurrence matrix from the set of R lists with putative haplotypes output by the HpltFind() function. CreateHpltOccTable() assumes that data originated from a diploid species.

Usage

CreateHpltOccTable(seq_table, filepath, 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.
filepath	is a user defined path to the folder where the output files from the HpltFind() function have been saved.
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 binary (logical) occurrence matrix with the data set sequences (inherited from seq_table) in columns and the putative haplotypes inferred by the HpltFind() function in rows.

See Also

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

Examples

seq_table <- sequence_table
filepath <- system.file("extdata/HpltFindOut/", package="MHCtools")
path_out <- tempdir()
CreateHpltOccTable(seq_table, filepath, path_out)

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