MHCtools: Analysis of MHC Data in Non-Model Species

Ten tools for bioinformatical processing and analysis of major histocompatibility complex (MHC) data. The functions are tailored for amplicon data sets that have been filtered using the 'dada2' method (for more information on 'dada2', visit <https://benjjneb.github.io/dada2/> ), but even other types of data sets can be analyzed. The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise comparisons of all sequences in a data set, and mean distances of all pairwise comparisons within each sample in a data set. The function additionally outputs five tables with physico-chemical z-descriptor values (based on Sandberg et al. 1998) for each amino acid position in all sequences in the data set. These tables may be useful for further downstream analyses, such as estimation of MHC supertypes. 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 ReplMatch() function matches replicates in data sets in order to evaluate genotyping success. The GetReplTable() and GetReplStats() functions perform such an evaluation. The CreateFas() function creates a fasta file with all the sequences in the data set. The CreateSamplesFas() function creates individual fasta files for each sample in the data set.

Version: 1.3.0
Depends: R (≥ 3.5.0)
Imports: stats, utils
Published: 2020-09-16
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved at biol.lu.se>
License: MIT + file LICENSE
NeedsCompilation: no
Materials: README NEWS
CRAN checks: MHCtools results

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Reference manual: MHCtools.pdf
Package source: MHCtools_1.3.0.tar.gz
Windows binaries: r-devel: MHCtools_1.3.0.zip, r-release: MHCtools_1.3.0.zip, r-oldrel: MHCtools_1.3.0.zip
macOS binaries: r-release: MHCtools_1.3.0.tgz, r-oldrel: MHCtools_1.3.0.tgz
Old sources: MHCtools archive

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