alleleconvert: Format conversion for codominant marker data
In prabclus: Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data

alleleconvert

R Documentation

Format conversion for codominant marker data

Description

Codominant marker data (which here means: data with several diploid loci; two alleles per locus) can be represented in various ways. This function converts the formats "genepop" and "structure" into "structurama" and "prabclus". "genepop" is a version of the format used by the package GENEPOP (Rousset, 2008), "structure" is a version of what is used by STRUCTURE (Pritchard et al., 2000), another one is "structureb". "structurama" is a version of what is used by STRUCTURAMA (Huelsenbeck and Andolfatto, 2007) and "prabclus" is required by the function alleleinit in the present package.

Usage

  alleleconvert(file=NULL,strmatrix=NULL, format.in="genepop",
                          format.out="prabclus",
                          alength=3,orig.nachar="000",new.nachar="-",
                          rows.are.individuals=TRUE, firstcolname=FALSE,
                          aletters=intToUtf8(c(65:90,97:122),multiple=TRUE),
                          outfile=NULL,skip=0)

Arguments

`file`	string. Filename of input file, see details. One of `file` and `strmatrix` needs to be specified.
`strmatrix`	matrix or data frame of strings, see details. One of `file` and `strmatrix` needs to be specified.
`format.in`	string. One of `"genepop"`, `"structure"`, or `"structureb"`, see details.
`format.out`	string. One of `"structurama"` or `"prabclus"`, see details.
`alength`	integer. If `format.in="genepop"`, length of code for a single allele.
`orig.nachar`	string. Code for missing values in input data.
`new.nachar`	string. Code for missing values in output data.
`rows.are.individuals`	logical. If `TRUE`, rows are interpreted as individuals and columns (variables if `strmatrix` is a data frame) as loci.
`firstcolname`	logical. If `TRUE`, it is assumed that the first column contains row names.
`aletters`	character vector. String of default characters for alleles if `format.out=="prabclus"` (the default is fine unless there is a locus that can have more than 62 different alleles in the dataset).
`outfile`	string. If specified, the output matrix (omitting quotes) is written to a file of this name (including row names if `fistcolname==TRUE`).
`skip`	number of rows to be skipped when reading data from a file (`skip`-argument of `read.table`).

Details

The formats are as follows (described is the format within R, i.e., for the input, the format of strmatrix; if file is specified, the file is read with read.table(file,colClasses="character") and should give the format explained below - note that colClasses="character" implies that quotes are not needed in the input file):

genepop: Alleles are coded by strings of length alength and there is no space between the two alleles in a locus, so a value of "258260" means that in the corresponding locus the two alleles have codes 258 and 260.
structure: Alleles are coded by strings of arbitrary length. Two rows correspond to each inidividual, the first row containing the first alleles in all loci and the second row containing the second ones.
structureb: Alleles are coded by strings of arbitrary length. One row corresponds to each inidividual, containing first and second alleles in all loci (first and second allele of first locus, first and second allele of second locus etc.). This starts in the third row (first two have locus names and other information).
structurama: Alleles are coded by strings of arbitrary length. the two alleles in each locus are written with brackets around them and a comma in between, so "258260" in "genepop" corresponds to "(258,260)" in "structurama".
prabclus: Alleles are coded by a single character and there is no space between the two alleles in a locus (e.g., "AC").

Value

A matrix of strings in the format specified as format.out with an attribute "alevels", a vector of all used allele codes if format.out=="prabclus", otherwise vector of allele codes of last locus.

Author(s)

Christian Hennig christian.hennig@unibo.it https://www.unibo.it/sitoweb/christian.hennig/en

References

Huelsenbeck, J. P., and P. Andolfatto (2007) Inference of population structure under a Dirichlet process model. Genetics 175, 1787-1802.

Pritchard, J. K., M. Stephens, and P. Donnelly (2000) Inference of population structure using multi-locus genotype data. Genetics 155, 945-959.

Rousset, F. (2008) genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources 8, 103-106.

Examples

  data(tetragonula)
# This uses example data file Heterotrigona_indoFO.dat
  str(alleleconvert(strmatrix=tetragonula))
  strucmatrix <-
    cbind(c("I1","I1","I2","I2","I3","I3"),
    c("122","144","122","122","144","144"),c("0","0","21","33","35","44"))
  alleleconvert(strmatrix=strucmatrix,format.in="structure",
    format.out="prabclus",orig.nachar="0",firstcolname=TRUE)
  alleleconvert(strmatrix=strucmatrix,format.in="structure",
    format.out="structurama",orig.nachar="0",new.nachar="-9",firstcolname=TRUE)

prabclus documentation built on Oct. 24, 2023, 1:06 a.m.