MHCtools

Analysis of MHC Data in Non-Model Species

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.

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Description file content

Package
MHCtools
Type
Package
Title
Analysis of MHC Data in Non-Model Species
Version
1.2.1
Description
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 ), 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.
License
MIT + file LICENSE
Encoding
UTF-8
LazyData
true
Imports
rlist (>= 0.4.6.1), utils
RoxygenNote
6.1.1
NeedsCompilation
no
Packaged
2019-08-09 16:53:05 UTC; jacobroved
Author
Jacob Roved [aut, cre]
Maintainer
Jacob Roved
Repository
CRAN
Date/Publication
2019-08-11 15:20:02 UTC

install.packages('MHCtools')

1.2.1

10 days ago

Jacob Roved

MIT + file LICENSE

Imports

rlist (>= 0.4.6.1), utils

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