HpltFind: HpltFind() function

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

HpltFind() function

Description

HpltFind is designed to automatically infer major histocompatibility complex (MHC) haplotypes from the genotypes of parents and offspring in families (defined as nests) in non-model species, where MHC sequence variants cannot be identified as belonging to individual loci. HpltFind() assumes that data originated from a diploid species. The functions GetHpltTable(), GetHpltStats(), and NestTablesXL() are designed to evaluate the output files.

Usage

HpltFind(nest_table, seq_table, alpha = 0.8, path_out)

Arguments

nest_table	is a table containing the sample names of parents and offspring in each nest. This table should be organized so that the individual names are in the first column (Sample_ID), and the nest number is in the second column (Nest). For each nest, the first two rows should be the parents, followed immediately by the offspring in the subsequent rows, and then followed by the next nest, and so on. It is assumed that nests are 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.
alpha	a numerical value between 0 and 1 (default 0.8) specifying a threshold by which a set of sequences overlapping between a chick and a parent will be assigned to the putative parental A haplotype or passed to the B haplotype. Typical values are in the range 0.6-0.9. In data sets with many different MHC alleles per individual (i.e. many MHC gene copies), alpha may be set high. In data sets with fewer MHC alleles per individual, it should be set lower. A range of alpha values may be tested to find the optimal setting for a given data set, e.g. by evaluating the mean proportion of incongruent sequences across the data set using GetHpltStats().
path_out	is a user defined path to the folder where the output files will be 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 set of R lists containing for each nest the putative haplotypes, the names of sequences that could not be resolved with certainty in each parent, the names of the sequences that were incongruent in the genotypes of the nest, and the mean proportion of incongruent sequences (which is a measure of the haplotype inference success and largely influenced by the exactness of the genotyping experiment). 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. Note: HpltFind() will overwrite any existing files with the same output file names in path_out.

See Also

GetHpltTable; GetHpltStats; NestTablesXL; CreateHpltOccTable; for more information about 'dada2' visit <https://benjjneb.github.io/dada2/>

Examples

nest_table <- nest_table
seq_table <- sequence_table
path_out <- tempdir()
HpltFind(nest_table, seq_table, alpha=0.8, path_out)

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