switch.alleles: Switch alleles in columns of a SnpMatrix or in test results
Description
This is a generic function which can be applied to objects of class
"SnpMatrix" or "XSnpMatrix" (which hold SNP genotype
data), or to objects of class
"SingleSnpTestsScore" or "GlmTests" (which hold
association test results). In the former case, specified SNPs can be
recoded as if the alleles were switched (so that AA genotypes
become BB and
vice-versa while AB remain unchanged). In the latter case,
test results are modified as if alleles had been switched.
Usage
switch.alleles(x, snps)
Arguments
x
The input object, of class "SnpMatrix",
"XSnpMatrix", "SingleSnpTestsScore", or
"GlmTests"
snps
A vector of type integer, character or logical specifying
the SNP to have its alleles switched