Package: MHCtools
Type: Package
Title: Analysis of MHC Data in Non-Model Species
Version: 1.2.1
Authors@R: person("Jacob", "Roved", email = "jacob.roved@biol.lu.se",
role = c("aut", "cre"))
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
<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.
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 <jacob.roved@biol.lu.se>
Repository: CRAN
Date/Publication: 2019-08-11 15:20:02 UTC

Description: 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
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 CreateSamplesFas() function creates individual fasta files for each sample in
Packaged: 2020-09-16 06:54:02 UTC; jacobroved