replicates_table

replicates_table and sequence_table_repl comprise a randomized dataset
derived from a real major histocompatibility complex (MHC) genotyping
experiment with technical replicates. The nucleotide sequences have been
replaced with randomly generated sequences, and sample names have been
anonymized.

datasets

Ten tools for analysis of major histocompatibility complex (MHC) data in non-
model species. The functions are tailored for amplicon data sets that have been
filtered using the 'dada2' method (for more information visit
<https://benjjneb.github.io/dada2>), but even other data sets can be analyzed,
if the data tables are formatted according to the description in each function.
The ReplMatch() function matches replicates in data sets in order to evaluate
genotyping success.
The GetReplTable() and GetReplStats() functions perform such an evaluation.
The HpltFind() function infers putative haplotypes from families in the data
set.
The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of
the haplotype inference.
The PapaDiv() function compares parent pairs in the data set and calculate their
joint MHC diversity, taking into account sequence variants that occur in both
parents.
The CalcPdist() function calculates the p-distances from pairwise comparisons of all
sequences in a data set, and mean p-distances of all pairwise comparisons within each
sample in a data set. The function includes the options to specify which codons to
compare and to calculate amino acid p-distances.
The CreateFas() function creates a fasta file with all the sequences in the data
set.
The CreateSamplesFas() function creates a fasta file for each sample in the data
set.

Jacob Roved

MHCtools

Analysis of MHC Data in Non-Model Species

replicates_table function

replicates_table is a data frame with 111 technical replicate samples
 in rows and 2 columns:<dl class="dl-horizontal">
<dt>Sample_ID</dt><dd>Technical replicate
 sample ID</dd> <dt>Replic_set</dt><dd>Index number of replicate set</dd> </dl>

Format

Data replicates_table — replicates_table

replicates_table is a data frame with 111 technical replicate samples
 in rows and 2 columns:<dl class='dl-horizontal'>
<dt>Sample_ID</dt><dd>Technical replicate
 sample ID</dd> <dt>Replic_set</dt><dd>Index number of replicate set</dd> </dl>

replicates_table: Data replicates_table

Description

Usage

Arguments

Format