| GetReplStats {MHCtools} | R Documentation |
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
Examples
filepath <- system.file("extdata/ReplMatchOut/", package="MHCtools")
GetReplStats(filepath)