This function takes a data table with genotypes ("AA", "AB", "BA" or
"BB") and converts them to their corresponding zygosity, i.e., to
homozygous ("hom") or heterozygous ("het").
The argument genotypes is expected to be a data table whose first column is
the SNP identifier, and remaining columns refer to samples on which the SNP
has been genotyped. All columns except the first should be factors, and
should contain the levels "AA", "AB", "BA" and "BB".
Note that this function changes its input by reference, meaning that the
variable passed as genotypes will be modified after running as_zygous().
This is for performance reasons.
Arguments
- genotypes
A data table whose first column is the SNP identifier (a character vector), and remaining columns refer to samples on which the SNP has been genotyped. All columns except the first should be factors, and should contain the levels
"AA","AB","BA"and"BB".
Value
A data table with the same structure as the data table passed in
genotypes. The only difference is that the sample columns (all except the
first) have their levels recoded to "hom" (homozygous) or "het"(heterozygous).
Examples
levels <- c("AA", "AB", "BA", "BB")
(df <- data.frame(
snp = c('rs123', 'rs456'),
sample01 = factor(c('AB', 'BA'), levels),
sample02 = factor(c('AA', 'BB'), levels)
))
#> snp sample01 sample02
#> 1 rs123 AB AA
#> 2 rs456 BA BB
as_zygous(df)
#> snp sample01 sample02
#> 1 rs123 het hom
#> 2 rs456 het hom
df
#> snp sample01 sample02
#> 1 rs123 het hom
#> 2 rs456 het hom