GetHpltTable {MHCtools}

GetHpltTable() function

Description

GetHpltTable uses the output files produced by the HpltFind() function to produce a table with the mean proportion of incongruent sequences for each nest. If the mean proportion of incongruent sequences is generally low, but certain nests have many incongruent sequences, biological reasons may be causing the mismatches, e.g. extra-pair fertilizations or recombination events.

Usage

GetHpltTable(filepath)

Arguments

filepath

is a user defined path to the folder where the output files from the HpltFind() function have been 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 table with the mean proportion of incongruent sequences for each nest.

See Also

HpltFind; GetHpltStats

Examples

filepath <- system.file("extdata/HpltFindOut/", package="MHCtools")
GetHpltTable(filepath)