Check SNP call rate

Source: R/utils_fQC.R

Identifies SNPs with call rates below a minimum threshold.

check.call.rate(summary, min.call.rate)

Arguments

summary

A data frame with SNP summary statistics (must contain `Call.rate` column).

min.call.rate

Numeric value specifying the minimum acceptable call rate.

Value

Character vector with SNP names below threshold. Returns `NULL` if none.

Author

Roberto Higa

Examples

df <- data.frame(Call.rate = c(0.85, 0.95), row.names = c("SNP1", "SNP2"))
check.call.rate(df, 0.9)
#> NULL