Description Usage Arguments Details Value See Also Examples
snpRecode
is a function to convert SNP genotypes to 0, 1, and 2 for the homozygous,
heterozygous, and other homozygous genotype, respectively.
1  snpRecode(snpG, designat)

snpG 
is a column vector in the genotypes array, created by 
designat 
is the 2base allele designations for each SNP. This is sometimes called allele report data, where the specefic bases of alleles A and B are reported. Formated as data frame with two factors for alleles A and B. See ‘Examples’. 
Recode snp genotypes by counting the number of copies of allele A in an element of snpG
which is a column vector in the genotypes array, ga
, where
snpG
is a column vector in the genotypes array,
ga
is the genotypes array created by toArray
. It contains elements such as "AA", "AG", "GA", "A", " ".
Unknown genotypes are those with non A/G/C/T bases, those are coded as 5.
A column vector of the integers 0, 1, and 2 is created based on the number of copies of allele A in each element of the supplied vector of genotypes. A value of 5 is used to indicate an unknown genotype.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20  ## Simulate random allele designations for 100 biallelic SNPs
set.seed(2016)
desig < array(sample(c('A','C','G','T'), size = 200, repl = TRUE), dim=c(100, 2))
## Simulate random SNP genotypes for 20 individuals  put them in array format
## '' indicates an unknown base
ga < array(0, dim=c(20, 100))
for(i in 1:20)
for(j in 1:100)
ga[i, j] < paste(sample(c(desig[j,],""), 2, prob=c(.46, .46, .08), repl=TRUE), collapse='')
## Recode the matrix, place recoded genotypes in ga.r
desig < data.frame(AlleleA_Forward = factor(desig[,1]), AlleleB_Forward = factor(desig[,2]))
ga.r < array(5, dim=c(20, 100))
for(i in 1:100) ga.r[,i] < snpRecode(ga[,i], desig[i,])
## Tabulate recoded genotypes in the matrix ga.r
table(ga.r)
# 0 1 2 5
# 326 632 701 341

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