scrime (version 1.2.9)

recodeSNPs: Recoding of SNP Values

Description

Recodes the values used to specify the genotypes of the SNPs to other values. Such a recoding might be required to use other functions contained in this package.

Usage

recodeSNPs(mat, first.ref = FALSE, geno = 1:3, snp.in.col = FALSE)

Arguments

mat

a matrix or data frame consisting of character strings of length 2 that specify the genotypes of the SNPs. Each of these character strings must be a combination of the letters A, T, C, and G. Missing values can be specified by "NN"

first.ref

does the first letter in the string coding the heterozygous genotype always stands for the more frequent allele? E.g., codes "CC" for the homozygous reference genotype if the genotypes of a SNP are coded by "CC", <

geno

a numeric or character vector of length 3 giving the three values that should be used to recode the genotypes. By default, geno = 1:3 which is the coding, e.g., required by rowChisqStats

snp.in.col

does each column of mat correspond to a SNP (and each row to an array)? If FALSE, it is assumed that each row represents a SNP, and each column an array.

Value

• A matrix of the same size as mat containing the recoded genotypes. (Missing values are coded by NA).

See Also

recodeAffySNP, snp2bin

Examples

# Generate an example data set consisting of 5 rows and 12 columns,
# where it is assumed that each row corresponds to a SNP.

mat <- matrix("", 10, 12)
mat[c(1, 4, 6),] <- sample(c("AA", "AT", "TT"), 18, TRUE)
mat[c(2, 3, 10),] <- sample(c("CC", "CG", "GG"), 18, TRUE)
mat[c(5, 8),] <- sample(c("GG", "GT", "TT"), 12, TRUE)
mat[c(7, 9),] <- sample(c("AA", "AC", "CC"), 12, TRUE)
mat

# Recode the SNPs

recodeSNPs(mat)

# Recode the SNPs by assuming that the first letter in
# the heterogyzous genotype refers to the major allele.

recodeSNPs(mat, first.ref = TRUE)