scrime: recodeAffySNP – R documentation

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recodeAffySNP

Recoding of Affymetrix SNP Values

Description

Recodes the values used on Affymetrix SNP chips to code the genotypes to other values – required, e.g., by other functions of this package.

Usage

recodeAffySNP(mat, refAA = FALSE, geno = 1:3)

Arguments

`mat`	a matrix or data frame consisting of the character strings `"AA"`, `"AB"`, `"BB"`. Missing values can be coded by either `"NN"` or `NA`. Each row is assumed to correspond to a variable, and each column to a microarray.
`refAA`	codes `"AA"` always for the homozygous reference genotype? If `TRUE`, `"AA"` is always replaced by `geno[1]`, and `"BB"` by `geno[3]`. If `FALSE`, it is evaluated rowwise whether `"AA"` or `"BB"` occurs more often, and the more frequently occuring value is set to `geno[1]`.
`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`.

Value

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

Examples

## Not run: 
# Generate a sample data set consisting of 10 rows and 12 columns,
# and randomly replace 5 of the values by "NN".

mat <- matrix("", 10, 12)
mat[1:5,] <- sample(c("AA", "AB", "BB"), 60, TRUE,
   prob = c(0.49, 0.42, 0.09))
mat[6:10,] <- sample(c("AA", "AB", "BB"), 60, TRUE,
   prob = c(0.09, 0.42, 0.49))
mat[sample(120, 5)] <- "NN"
mat

# Recode the SNPs.

recodeAffySNP(mat)

# Recode the SNPs assuming that "A" is always the major allele.

recodeAffySNP(mat, refAA = TRUE)


## End(Not run)

scrime

Analysis of High-Dimensional Categorical Data Such as SNP Data

v1.3.5

GPL-2

Authors

Holger Schwender, with a contribution of Arno Fritsch

Initial release

2018-12-01