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Filter Genotype Matrix Based on Parental Genotype

Source: R/filter_geno_by_parents.R
filter_geno_by_parents.Rd

filter_geno_by_parents filters a genotype matrix to retain only homozygous polymorphic markers between two specified parents. It removes markers that do not meet the homozygous polymorphism criteria (P1 = 0 & P2 = 2 or P1 = 2 & P2 = 0).

Usage

filter_geno_by_parents(geno, parent1, parent2)

Arguments

geno

A genotype matrix or data frame where markers are rows and individuals are columns. Must be coercible to a data frame.

parent1

Character. The name of the column representing the first parent.

parent2

Character. The name of the column representing the second parent.

Value

A filtered data frame containing only markers that are homozygous polymorphic between the two parents.

Details

  • Retains markers where parent1 is 0 and parent2 is 2 (A × B) or parent1 is 2 and parent2 is 0 (B × A). See the methods section of Braun et al. 2017 for more info on marker types. The Plant Genome Vol. 10 No. 3.

Examples

# Example genotype matrix
geno_data <- data.frame(
  Marker1 = c(0, 1, 2, 0, 2),
  Marker2 = c(2, 0, 2, 1, 0),
  Parent1 = c(0, 2, 2, 0, 2),
  Parent2 = c(2, 0, 0, 2, 0)
)

# Filter markers based on parents
filtered_geno <- filter_geno_by_parents(geno_data, "Parent1", "Parent2")
print(filtered_geno)
#>   Marker1 Marker2 Parent1 Parent2
#> 1       0       2       0       2
#> 2       1       0       2       0
#> 3       2       2       2       0
#> 4       0       1       0       2
#> 5       2       0       2       0