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