rplot: Recombination Plot

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

Recombination Plot

Description

This function creates a plot which shows the sum of all recombination events across a half-sib family.

Usage

rplot(x, distance, start = 1, end = ncol(x), maximum = 100,
overwrite = FALSE, method = "constant")

Arguments

x	matrix of 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).
distance	integer of physical distances between markers
start	integer first marker selected for the plot
end	integer last marker selected for the plot
maximum	integer maximum number of recombinations to show (higher recombination rates will be omitted from the plot)
overwrite	logical draw a diagram over the current diagram (default FALSE)
method	character please refer to the pm document

Examples

genotype <- matrix(c(
0,2,0,1,0,
2,0,1,2,2,
2,2,1,0,2,
2,2,1,1,1,
0,0,2,1,0), ncol = 5, byrow = TRUE) # each row contains the SNP of individuals

rplot(genotype, c(1,2,3,4,8)) 

hsphase documentation built on May 29, 2024, 2:20 a.m.