Package: MHCtools
Type: Package
Title: Analysis of MHC Data in Non-Model Species
Version: 1.2.0
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 analysed, 
    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: 2019-08-08 14:49:56 UTC; jacobroved
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved@biol.lu.se>
Repository: CRAN
Date/Publication: 2019-08-08 16:40:05 UTC
