checkGenotypeFile {nprcgenekeepr} | R Documentation |
Check genotype file
Description
Checks to ensure the content and structure are appropriate for a genotype file. These checks are simply based on expected columns and legal domains.
Usage
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
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")
}
)
[Package nprcgenekeepr version 1.0.7 Index]