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. The
functions GetHpltTable() and GetHpltStats() are designed to evaluate the
output files.
HpltFind(nest_table, seq_table, path_out)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 is a sequence table as output by the 'dada2' pipeline, which has samples in rows and nucleotide sequence variants in columns.
is a user defined path to the folder where the output files will be saved.
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 using e.g. the list.load() function in the 'rlist' package.
GetHpltTable; GetHpltStats; for more
information about 'dada2' visit <https://benjjneb.github.io/dada2>
# NOT RUN {
nest_table <- nest_table
seq_table <- sequence_table
path_out <- tempdir()
HpltFind(nest_table, seq_table, path_out)
# }
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