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. The function stops (an error, not a warning) when the dataframe has fewer than three columns, when the first column name does not contain "id" (any case), when any column is named first or second (any case), or when an allele in columns 2 or 3 that reads as an integer is above 10000 (it would collide with the integer codes addGenotype assigns).

Usage

checkGenotypeFile(genotype)

Arguments

genotype

dataframe with genotype data

Value

The genotype dataframe, checked for the column count, the first column's name and the allele range described above; no column types are checked. 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