HapEstXXR (version 0.1-8)

allele1to2: Convert genotype matrix from two different types

Description

(not supported for x-linked markers)

Usage

allele1to2(geno, marker.label = NULL, miss.val = NA)
allele2to1(geno, marker.label = NULL, miss.val = NA)
alleleRto1(geno, marker.label = NULL, miss.val = NA)
alleleRto2(geno, marker.label = NULL, miss.val = NA)
allele1toR(geno, marker.label = NULL, miss.val = c(-1, NA))
allele2toR(geno, marker.label = NULL, miss.val = NA)

Arguments

geno

(m,n)-genotype matrix m=number of individuals type 1 and R: n=number of snps type 2: n=2*number of snps

marker.label

Vector of labels for marker, If a marker name is "SNP", its columns will be "SNP.1" and "SNP.2"

miss.val

Vector of specified missing values.

Value

converted genotype matrix

Details

3 different types of genotype matrices: Type 1 : 1-column genotype matrix : minor allele count (0,1,2) Type 2 : 2-column genotype matrix : each marker has a pair of two columns (1/1, 1/2, 2/2) Type R : 1-column genotype matrix : code (1 = 1/1, 3 = 1/2, 2 = 2/2)

Examples

 ## [A] allele1to2
 N <- 10
 ns <- 4
 (geno <- matrix(sample(c(NA, 0:2), N * ns, replace = TRUE), nc = ns))
 allele1to2(geno)

 ## [B] allele2to1
 (geno <- matrix(c(0, 0, 1, 1, 2, 1, 1, 2,
                   1, 1, 2, 2, 2, 2, 1, 2,
                   0, 0, 1, 1, 2, 1, 0, 0), nc = 4, byrow = TRUE))
 allele2to1(geno)

 ## [C] alleleRto1
 N <- 10
 ns <- 4
 (geno <- matrix(sample(c(NA, 1:3), N * ns, replace = TRUE), nc = ns))
 alleleRto1(geno)

 ## [D] alleleRto2
 N <- 10
 ns <- 4
 (geno <- matrix(sample(c(0, 1:3), N * ns, replace = TRUE), nc = ns))
 alleleRto2(geno)

 ## [E] allele1toR
 N <- 10
 ns <- 4
 (geno <- matrix(sample(c(NA, 0:2), N * ns, replace = TRUE), nc = ns))
 allele1toR(geno)

 ## [F] allele2toR
 (geno <- matrix(c(0, 0, 1, 1, 2, 1, 1, 2, 1, 1, 2, 2, 2, 2, 1, 2, 
                   0, 0, 1, 1, 2, 1, 0, 0),
     nc = 4, byrow = TRUE))
 allele2toR (geno)