GetReplStats: GetReplStats function

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

GetReplStats function

Description

GetReplStats uses the output files produced by the ReplMatch() function to calculate statistics on the agreement between replicated samples in the sequencing experiment.

Usage

GetReplStats(filepath)

Arguments

filepath

is a user defined path to the folder where the output files from the ReplMatch() 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 list containing the number of replicate sets with zero incongruent sequences, the proportion of replicate sets with zero incongruent sequences, the mean of the mean proportion of incongruent sequences across all replicate sets, and the repeatability of the sequencing experiment.

See Also

ReplMatch; GetReplTable

Examples

filepath <- system.file("extdata/ReplMatchOut/", package="MHCtools")
GetReplStats(filepath)

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