HpltMatch: HpltMatch() function

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

HpltMatch() function

Description

Putative haplotypes may be identical to each other, or they may differ only by incongruent or unresolved sequences. It is therefore useful to curate putative haplotypes by comparing them to identify potentially overlapping types as candidates for further investigation. HpltMatch calculates the proportion of matching sequences between pairs of haplotypes and produces a .csv table with values in a lower left matrix. If a threshold value is specified, a list of haplotype matches where the proportion of matching sequences exceeds the threshold will be produced.

Usage

HpltMatch(hplt_occ_matrix, path_out, threshold = NULL)

Arguments

hplt_occ_matrix	A binary (logical) occurrence matrix with the data set sequences in columns and the putative haplotypes in rows, as produced by the CreateHpltOccTable() function.
path_out	a user defined path to the folder where the output file(s) will be saved.
threshold	a numerical value between 0 and 1 (default NULL) specifying a threshold for the proportion of matching sequences between haplotypes.

Details

Note: The NestTablesXL() function provides a useful format for further investigation of potentially overlapping haplotypes.

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 table specifying the proportions of matching sequences between pairs of haplotypes (in a lower left matrix). If a threshold value is specified, a list of haplotype matches where the proportion of matching sequences exceeds the threshold will be printed to the console. The list will also be saved in the output path, and can be reopened in R e.g. using the readRDS() function in the base package. Note: HpltMatch() will overwrite any existing files with the same output file names in path_out.

See Also

HpltFind; CreateHpltOccTable; NestTablesXL

Examples

hplt_occ_matrix <- hplt_occurrence_matrix
path_out <- tempdir()
HpltMatch(hplt_occ_matrix, path_out, threshold=NULL)

MHCtools documentation built on July 9, 2023, 5:13 p.m.