Query genotypes for heterozygotes
Query a matrix of genotypes for heterozygotes
is_het(x, na_is_false = TRUE) is.het(x, na_is_false = TRUE)
x |
a matrix of genotypes |
na_is_false |
should missing data be returned as NA (FALSE) or FALSE (TRUE) |
This function was designed to identify heterozygous positions in a matrix of genotypes.
The matrix of genotypes can be created with extract.gt.
Because the goal was to identify heterozygotes it may be reasonable to ignore missing values by setting na_is_false to TRUE so that the resulting matrix will consist of only TRUE and FALSE.
In order to preserve missing data as missing na_is_false can be set to FALSE where if at least one allele is missing NA is returned.
data(vcfR_test) gt <- extract.gt(vcfR_test) hets <- is_het(gt) # Censor non-heterozygous positions. is.na(vcfR_test@gt[,-1][!hets]) <- TRUE
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