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Genind 2 Hierfstat

This R function converts genind objects from the adegenet package into a hierfstat data frame. It takes a genind object and population information as inputs. It returns a data frame with nloci+1 columns, with the first column containing population identifiers and following columns containing genotypes at each locus. The genotypes are converted to numeric format for analysis in hierfstat.

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Gabriel Dequigiovanni
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138 views2 pages

Genind 2 Hierfstat

This R function converts genind objects from the adegenet package into a hierfstat data frame. It takes a genind object and population information as inputs. It returns a data frame with nloci+1 columns, with the first column containing population identifiers and following columns containing genotypes at each locus. The genotypes are converted to numeric format for analysis in hierfstat.

Uploaded by

Gabriel Dequigiovanni
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as TXT, PDF, TXT or read online on Scribd
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########################################################

#' @title Converts genind objects from adegenet into a hierfstat data frame
#' @description Converts genind objects from adegenet into a hierfstat data frame
#' @usage genind2hierfstat(dat,pop=NULL)
#' @param dat a genind object
#' @param pop a vector containing the population to which each individual belongs.
#' If pop=NULL, pop taken from slot pop of the genind object
#'
#' @return a data frame with nloci+1 columns and ninds rows. The first column
#' contains the population identifier, the following the genotypes at each locus
#'
#' @examples
#'
#' \dontrun{
#' library(adegenet)
#' data(nancycats)
#' genind2hierfstat(nancycats)
#' basic.stats(nancycats)
#' genet.dist(nancycats)
#' data(H3N2)
#' basic.stats(genind2hierfstat(H3N2,pop=rep(1,dim(H3N2@@tab)[1])),diploid=FALSE)
#' }
#'
#' @export
##########################################################
genind2hierfstat<-function(dat,pop=NULL){
if (!is.genind(dat)) stop("dat must be a genind object. Exiting")

if(is.null(pop)){
if (is.null(adegenet::pop(dat))){
stop("population factor must be defined")
} else {
pop <- adegenet::pop(dat)
}
}

if (dat@type!="codom") stop("data type must be codominant. Exiting")


ploid<-unique(dat@ploidy)
if (length(ploid)!=1) stop("data must contain only diploids or only haploids.
Exiting")
if (ploid>2L) stop("Data must come from diploids or haploids. Exiting")
alleles.name<-toupper(unique(unlist(adegenet::alleles(dat))))
ids <- adegenet::indNames(dat)

# convert alleles
x <- if(!all(alleles.name %in% c("A", "C", "G", "T"))) {
if(length(grep("[[:alpha:]|[:punct:]]", alleles.name)) > 0) {
# for loci where alleles are not all numeric nor all nucleotides
max.length <- max(sapply(alleles(dat), length))
digits <- floor(log10(max.length))
dat <- as.matrix(genind2df(dat, sep = "", usepop = FALSE,
oneColPerAll = TRUE))
dat <- apply(dat, 2, function(a) ifelse(a == "NA", NA, a))
# cycle through each locus
do.call(cbind, lapply(seq(ploid, ncol(dat), by = ploid),
function(end) {
start <- end - ploid + 1
allelesid <- sort(unique(as.vector(dat[, start:end])))
# match alleles of each genotype with sorted order: index is new
allele
apply(dat[, start:end, drop = FALSE], 1, function(gntp) {
if(any(is.na(gntp))) return(NA)
gntp <- match(gntp, allelesid)
# zero pad numeric alleles and return collapsed genotype
gntp <- formatC(gntp, digits = digits, flag = "0", mode
="integer")
as.integer(paste(gntp, collapse = ""))
})
}))
}
else { # all alleles are numeric
# check if all alleles code have same number of digits
tmp1<-unique(nchar(unlist([email protected])))
if (length(tmp1)>1){
dig<-max(tmp1)
allnames<-lapply([email protected],formatC,width=dig,flag="0",mode="integer")
[email protected]<-allnames
}
dat <- genind2df(dat, sep = "", usepop = FALSE)
do.call(cbind, lapply(dat, as.integer))
}
} else { # all alleles are nucleotides
dat <- genind2df(dat, sep = "", usepop = FALSE)
do.call(cbind, lapply(dat, function(a) {
a <- gsub("[aA]", "1", a)
a <- gsub("[cC]", "2", a)
a <- gsub("[gG]", "3", a)
a <- gsub("[tT]", "4", a)
as.integer(a)
}))
}
x<-data.frame(pop=pop,x)
rownames(x) <- ids
return(x)
}

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