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Flexible Genotype Format Converter (Supports Polyploid Dosage)

Source: R/formater_flex.R
formater_flex.Rd

Converts genotype data between character string formats (e.g., "AABB", "ABBB") and numeric dosage values (e.g., 0, 1, 2, 3) based on user-defined reference and alternative alleles. This function is designed to handle diploid and polyploid genotypes by interpreting the number of occurrences of the alternative allele.

This is especially useful for genotype encodings that represent dosage via string repetition (e.g., "AAAB" → 1 alt allele), or to reconstruct genotype strings from numeric dosage values (e.g., 0 → "AAAA").

Usage

formater_flex(
  geno,
  to_numeric = TRUE,
  ref_allele = "A",
  alt_allele = "B",
  ploidy = 2
)

Arguments

geno

A data frame containing genotype values. Values must be either character strings representing genotypes (e.g., "AAAA", "AAAB", "BBBB"), or numeric dosage values (e.g., 0 to ploidy).

to_numeric

Logical. If TRUE, converts character genotypes to numeric dosage by counting the number of alt_allele occurrences. If FALSE, reconstructs genotype strings from numeric dosage values using the specified ref_allele and alt_allele.

ref_allele

Character. The reference allele. This is used to define the "zero dosage" baseline and for reconstructing character genotypes from numeric dosage (e.g., "A" in "AAAB").

alt_allele

Character. The alternative allele. Dosage is computed as the count of this allele in the genotype string (e.g., "B" in "AAAB" → dosage = 1).

ploidy

Integer. Ploidy level of the organism. Only used when to_numeric = FALSE to determine how many reference and alternative alleles to paste together when reconstructing genotype strings.

Value

A data frame of the same structure as geno, with genotypes converted according to the to_numeric setting.

Details

  • When to_numeric = TRUE, all values in geno must be character strings, and the function will count the number of occurrences of the alt_allele using stringr::str_count(). Missing values (NA) are preserved.

  • When to_numeric = FALSE, all values in geno must be numeric dosages between 0 and ploidy, inclusive. The function will reconstruct character genotype strings by repeating the ref_allele and alt_allele the appropriate number of times. For example, with ploidy = 4, a dosage of 2 becomes "AABB".

  • Values outside the expected range (e.g., dosage > ploidy or unknown characters) are converted to NA.

Examples

# Example 1: Character to numeric (tetraploid)
if (FALSE) { # \dontrun{
geno <- data.frame(
  Marker1 = c("AAAA", "AAAB", "AABB", "ABBB", "BBBB"),
  Marker2 = c("AAAB", "AABB", "ABBB", "BBBB", NA)
)
formater_flex(geno, to_numeric = TRUE, ref_allele = "A", alt_allele = "B")
} # }
# Example 2: Numeric to character (tetraploid)
 if (FALSE) { # \dontrun{
dosage <- data.frame(
  Marker1 = c(0, 1, 2, 3, 4),
  Marker2 = c(1, 2, 3, 4, NA)
)
formater_flex(dosage, to_numeric = FALSE, ref_allele = "A", alt_allele = "B", ploidy = 4)
} # }