MakeCounts {HardyWeinberg}

Create genotype counts from bi-allelic marker data

Description

MakeCounts creates a matrix of genotype counts, with one row for each bi-allelic marker, containing 4 columns with the counts AA, AB, BB and NA (missings) respectively

Usage

MakeCounts(X, alleles, pos1 = 1, pos2 = 3, coding = c(AA=0,AB=1,BB=2), sep = "")

Arguments

X

A matrix or dataframe with bi-allelic genotyping information, markers in columns, individuals in rows

alleles

a vector of alleles for each marker (e.g. c("A/T","A/G",...)). Only relevanit if X is a matrix with text entries.

pos1

position of the first allele in the allele string (1 by default)

pos2

position of the second allele in the allele string (3 by default)

coding

indicates how homozygotes and heterozygote are coded as numbers. Only relevant if X is a matrix with numeric entries.

sep

allele separator character for genotype data in text format ("" for AA; "/" for "A/A")

Details

MakeCounts is thought for bi-allelic marker data only. Missings are should be coded by NA. It produces the right input for HWTernaryPlot.

Heterozygotes may be coded in the data as "AB" or "BA". Both entries will be counted as a heterozygote.

Value

A matrix of 4 columns

Author(s)

Jan Graffelman [e-mail]

See Also

HWTernaryPlot

Examples

SNP1 <- c("GG","GG","GG","GG","GG","GG","GG","GG","GG")
SNP2 <- c("CG","GG","CC","GG","GG","CG","CG","CG","CG")
SNP3 <- c("AA","AA","AA","AG","AA","AG","AA","AA","AA")
SNP4 <- c("GG","GG","GG","GG","GG","GG","GG","GG","GG")
SNP5 <- c("CC","CC","CC","CC","CC","CC","CT","CT","CT")
X <- cbind(SNP1,SNP2,SNP3,SNP4,SNP5)
Y <- MakeCounts(X,c("A/G","C/G","A/G","A/G","C/T"))
print(Y)
W <- matrix(sample(c(0,1,2,NA),100,replace=TRUE),ncol=5)
Z <- MakeCounts(W,coding=c(0,1,2))