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. (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 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)