PapaDiv: PapaDiv() function

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

PapaDiv() function

Description

PapaDiv calculates the joint major histocompatibility complex (MHC) diversity in parent pairs, taking into account alleles that are shared between the parents. The joint diversity in parent pairs is often of interest in studies of mate choice, fitness, and heritability.

Usage

PapaDiv(parents_table, seq_table, path_out)

Arguments

parents_table	is a table containing the sample names of the parents in each nest. This table should be organized so that each row represents one nest, with the individual names of the mothers in the first column (Mother), and the individual names of the fathers in the second column (Father).
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

The PapaDiv() function outputs a set of R lists containing for the joint diversity of each parent pair, the proportion of sequences that are shared between the parents, the diversity of each of the parents, the observed sequence variants in each parent, the matched sequence variants, and the incongruent sequence variants in each parent.

In addition, PapaDiv() produces a summary table with the names of the parents in a pair, their respective MHC diversities, and the joint parent pair diversity.

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 the joint diversity of each parent pair, the proportion of sequences that are shared between the parents, the diversity of each of the parents, the observed sequence variants in each parent, the matched sequence variants, and the incongruent sequence variants in each parent. 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 are saved in a sub folder in the output path called Parent_pairs (created by PapaDiv()) and can be reopened in R e.g. using the readRDS() function in the base package. For downstream data analysis, the PapaDiv() function also produces a summary table with the names of the parents in a pair, their respective MHC diversities, and the joint parent pair diversity. This table is saved as a .csv file in the output path.

See Also

For more information about 'dada2' visit <https://benjjneb.github.io/dada2/>

Examples

parents_table <- parents_table
seq_table <- sequence_table
path_out <- tempdir()
PapaDiv(parents_table, seq_table, path_out)

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