Check SNP Hardy-Weinberg equilibrium deviation

Source: R/utils_fQC.R

Identifies SNPs deviating from HWE beyond a z-score threshold.

check.snp.hwe(snp.summary, max.dev)

Arguments

snp.summary

Data frame with SNP summary (must contain `z.HWE` column).

max.dev

Maximum z-score allowed.

Value

Character vector with SNP names deviating from HWE. Returns `NULL` if none.

Author

Roberto Higa

Examples

df <- data.frame(z.HWE = c(2, 5), row.names = c("SNP1", "SNP2"))
check.snp.hwe(df, 3)
#> NULL