co {hsphase}

Crossover Detection

Description

Detect all possible crossover events.

Usage

co(genotypeMatrix)

Arguments

genotypeMatrix

matrix half-sib genotypes (one half-sib per row, with SNP ordered by mapping position in the columns. Data should be numeric. Use 0, 1 and 2 for respectively AA, AB and BB. Use 9 for missing data)

Value

Returns a matrix with the number of crossover events for each site.

Examples

genotype <- matrix(c(           # Define a Half-sib Genotype Matrix
  2,1,0,                        # Individual 1
  2,0,2,                        # Individual 2
  0,0,2                         # Individual 3
  ), byrow = TRUE, ncol = 3)    # There are 3 individuals with three SNPs
  
co(genotype)