alleleSplit: Split Alleles For Diploid Data

In strataG: Summaries and Population Structure Analyses of Genetic Data

Description

Split loci stored in one column to two columns for each allele in a matrix of diploid data.

Usage

alleleSplit(x, sep = NULL)

Arguments

x	a matrix or data.frame containing diploid data. Every column represents one locus with two alleles.
sep	separator used between alleles of a locus. If NULL, then alleles should be of equal length (e.g., 145095 = 145 and 095, or AG = A and G).

Value

matrix with alleles for each locus in one column split into separate columns.

Author(s)

Eric Archer [e-mail]

Examples

# A sample SNP data set with no separators between nucleotides in a genotype
snps <- do.call(cbind, lapply(1:3, function(i) {
  a1 <- sample(c("A", "G"), 10, rep = TRUE)
  a2 <- sample(c("A", "G"), 10, rep = TRUE)
  paste(a1, a2, sep = "")
}))
colnames(snps) <- paste("Loc", LETTERS[1:3], sep = "_")
snps
alleleSplit(snps)

# A sample microsatellie data set with alleles separated by "/"
alleles <- seq(100, 150, 2)
msats <- do.call(cbind, lapply(1:3, function(i) {
  a1 <- sample(alleles, 10, rep = TRUE)
  a2 <- sample(alleles, 10, rep = TRUE)
  paste(a1, "/", a2, sep = "")
}))
colnames(msats) <- paste("Loc", LETTERS[1:3], sep = "_")
msats
alleleSplit(msats, sep = "/")

strataG documentation built on Feb. 28, 2020, 9:07 a.m.