rplot {hsphase}

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))