Check genotype file

Checks to ensure the content and structure are appropriate for a genotype file. These checks are simply based on expected columns and legal domains.

checkGenotypeFile(genotype)

Arguments

genotype	dataframe with genotype data

Value

A genotype file that has been checked to ensure the column types and number required are present. The returned genotype file has the first column name forced to "id".

Examples

# \donttest{
library(nprcgenekeepr)
ped <- nprcgenekeepr::qcPed
ped <- ped[order(ped$id), ]
genotype <- data.frame(id = ped$id[50 + 1:20],
                       first_name = paste0("first_name", 1:20),
                       second_name = paste0("second_name", 1:20),
                       stringsAsFactors = FALSE)

## checkGenotypeFile disallows dataframe with < 3 columns
tryCatch({
  checkGenotypeFile(genotype[ , c("id", "first_name")])
  }, warning = function(w) {
    cat("Warning produced")
  }, error = function(e) {
    cat("Error produced")
})
#> Error produced
# }