atcg1234BackTransform: Letter to number converter

In enhancer: Mixed-Effects Models Enhancing Functions

Letter to number converter

Description

This function was designed to help users back transform the numeric marker matrices from the function atcg1234 into letters.

Usage

atcg1234BackTransform(marks, refs)

Arguments

marks	a centered marker matrix coming from atcg1234.
refs	a 2 x m matrix for m markers (columns) and 2 rows where the reference and alternate alleles for each marker are indicated.

Value

markers

a new marker matrix leter coded according to the reference allele matrix.

Author(s)

Giovanny Covarrubias-Pazaran

Examples

genotypes <- rbind(
  c("AAAG"  ,   "AAGG"  ,   "TTCC"  ,   "TTTT"  ,   "CCCC"),
  c("AAGG"  ,  "AGGG"   ,  "TTCC"   ,  "TTTT"   ,  "TCCC"),
  c("AAGG"  ,   "GGGG"  ,   "TTCC"  ,   "TTTT"  ,   NA),
  c("AAAA"  ,   "GGGG"  ,   "CCCC"  ,   "TTTT"  ,   NA),
  c("AAAA"  ,   "GGGG"  ,   "CCCC"  ,   "TTCC"  ,   NA)
)
rownames(genotypes) <- letters[1:5]
colnames(genotypes) <- paste0("m",1:5)

## convert markers to numeric format polyploid potatoes
numo <- atcg1234(data=genotypes, ploidy=4)
numo

## convert markers back to letters
Xb <- atcg1234BackTransform(marks= numo$M, refs= numo$ref.alleles)
Xb

enhancer documentation built on April 12, 2026, 9:07 a.m.