Extracts lines that have a combination of favorable alleles across target loci.

Usage

find_lines(mat, present = character(), absent = character())

Arguments

mat: A binary matrix/data frame with 1s and 0s. Rows = lines, Columns = target loci.
present: Character vector of column names that must be 1 (present).
absent: Character vector of column names that must be 0 (absent).

Value

Character vector of lines matching the intersection criteria.

Examples

# \donttest{
# example code
library(panGenomeBreedr)

# Marker genotype data
geno <- data.frame(SNP1 = c("A:A", "A:G", "G:G", "A:A"),
                   SNP2 = c("C:C", "C:T", "T:T", "C:T"),
                   SNP3 = c("G:G", "G:G", "A:G", "A:A"),
                   row.names = c("Line1", "Line2", "Line3", "Line4"))

# Trait predictive markers meta data
marker_info <- data.frame(qtl_markers = paste0('SNP', 1:3),
                          fav_alleles = c('A', 'C', 'G'),
                          alt_alleles = c('G', 'T', 'A'))

# Select lines where genotype is either homozygous for favorable alleles at all loci
foreground_select(geno_data = geno,
                  fore_marker_info = marker_info,
                  fore_marker_col = 'qtl_markers',
                  fav_allele_col = 'fav_alleles',
                  alt_allele_col = 'alt_alleles',
                  select_type = "homo") |>

                  find_lines(present = colnames(geno))
#> [1] "Line1"



# }