checkGenotypeFile: Check genotype file

In rmsharp/nprcmanager: Genetic Tools for Colony Management

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")
})

rmsharp/nprcmanager documentation built on Feb. 2, 2025, 12:45 a.m.