ReplMatch {MHCtools}

ReplMatch() function

Description

In amplicon filtering it is sometimes valuable to compare technical replicates in order to estimate the accuracy of a genotyping experiment. This may be done both to optimize filtering settings and to estimate repeatability to report in a publication. ReplMatch is designed to automatically compare technical replicates in an amplicon filtering data set and report the proportion of mismatches. The functions GetReplTable() and GetReplStats() are designed to evaluate the output files.

Usage

ReplMatch(repl_table, seq_table, path_out)

Arguments

repl_table

is a table containing the sample names of technical replicates in the data set. This table should be organized so that the individual names are in the first column (Sample_ID), and the index number of the replicate set is in the second column (Replic_set). Replicate sets may contain more than two replicates, but sets must be numbered consecutively beginning at 1.

seq_table

seq_table is a sequence table as output by the 'dada2' pipeline, which has samples in rows and nucleotide sequence variants in columns.

path_out

is a user defined path to the folder where the output files will be saved.

Details

Note: ReplMatch() will throw a warning if all samples in a replicate set have 0 sequences. In that case, the mean_props for that replicate set and the repeatability for the data set will be NaN, and ReplMatch() will report which replicate set is problematic and suggest to remove it from the repl_table. If removing replicate sets, beware that the replicate sets in repl_table must be numbered consecutively beginning at 1.

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 set of R lists containing for each replicate set the observed sequence variants, the names of the sequences that were incongruent in the replicates, and the mean proportion of incongruent sequences (if 100 matches are expected between the replicates, this is equivalent of an error rate in the sequencing process). The sequences are named in the output by an index number corresponding to their column number in the sequence table, thus identical sequences will have identical sample names in all the output files. These files can be reopened in R e.g. using the readRDS() function in the base package.

See Also

GetReplTable; GetReplStats; for more information about 'dada2' visit <https://benjjneb.github.io/dada2/>

Examples

repl_table <- replicates_table
seq_table <- sequence_table_repl
path_out <- tempdir()
ReplMatch(repl_table, seq_table, path_out)