NestTablesXL {MHCtools}

NestTablesXL() function

Description

NestTablesXL reads the R lists output by the HpltFind() function and translates them to an Excel workbook for more convenient evaluation of the inferred haplotypes and curation of unresolved and incongruent sequences. The workbook contains separate tabs for each nest in the data set and provides an overview of the genotypes of the samples in each nest and the inferred haplotypes.

Usage

NestTablesXL(nest_table, seq_table, filepath, 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. Please use the same table as was used to generate the haplotypes using HpltFind().

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. Please use the same table as was used to generate the haplotypes using HpltFind().

filepath

is a user defined path to the folder where the output files from the HpltFind() function have been saved.

path_out

is a user defined path to the folder where the output file 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

An Excel workbook with individual tabs for each nest in nest_table. Each tab contains a binary (logical) occurrence matrix with the samples from each nest in columns and sequences (inherited from seq_table) in rows. The order of the samples is derived from nest_table, with parents in the two leftmost columns. Each tab also lists the putative haplotypes inferred by the HpltFind() function and provides lists of unresolved sequences in haplotypes, sequences with unidentified decent (i.e., present in parents but not in offspring), sequences not assigned to haplotypes, and sequences with unidentified origin (i.e., present in offspring but not in parents). Note: NestTablesXL() will overwrite any existing file with the output file name in path_out.

See Also

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

Examples

nest_table <- nest_table
seq_table <- sequence_table_hplt
filepath <- system.file("extdata/HpltFindOut/", package="MHCtools")
path_out <- tempdir()
NestTablesXL(nest_table, seq_table, filepath, path_out)