recodeSNPs: Recoding of SNP Values
In scrime: Analysis of High-Dimensional Categorical Data Such as SNP Data

Description Usage Arguments Value See Also Examples

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.

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

`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"` or `NA`. Depending on `snp.in.col` it is assumed that each row of `mat` represents a SNP and each column a variable (`snp.in.col = FALSE`), or vice versa.
`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"`, `"CG"` and `"GG"`? If `TRUE`, the value made up only of this first letter is set to `geno[1]`, and the value made up only of the second letter is set to `geno[3]`. If `FALSE`, it is evaluated rowwise which of the homozygous genotypes has the higher frequency and the more often occuring value is set to `geno[1]`, and the other to `geno[3]`.
`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` or `pamCat`.
`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.

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

recodeAffySNP, snp2bin

## Not run: 
# 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)


## End(Not run)