mpMap (version 1.14)

mapcomp: Functions for comparison of two map orders

Description

Takes in two maps with the aim of comparing the position of common markers. Creates a mapcomp object for plotting and summary.

Usage

mapcomp(object1, object2) 
"plot"(x, ...)
"summary"(object, ...)

Arguments

object1

Object inheriting class mpcross or class map

object2

Object inheriting class mpcross or class map

object

Object of class mapcomp for summarizing

x

Object of class mapcomp

...

Additional arguments

Value

An object of class mapcomp with components:

commonmrk

A matrix containing 5 columns with the names of all common markers for the two maps (mname), the chromosome mapped to in the first map (chr1), the position mapped to in the first map (pos1), the chromosome mapped to in the second map (chr2) and the position mapped to in the second map (pos2)

samechr

A matrix containing 5 columns as above. Differs from commonmrk in that duplicated markers in either map will have been removed, so all markers map to exactly one chromosome

map1

The first map - either the originally input object1, or object1$map if it inherits class mpcross

map2

The first map - either the originally input object2, or object2$map if it inherits class mpcross

correlations

The correlation between positions in map1 and map2 for each chromosome

dup1

The names of markers duplicated in map1

dup2

The names of markers duplicated in map2

Plot produces for a comparison for each chromosome of positions of markers which are mapped to that chromosome in both mapsSummary function returns printed summary including - number of markers in each map; number of markers common to both maps; number of duplicated markers in each map; number of markers mapped to different chromosomes; correlations between positions on each chromosome.

Examples

map1 <- sim.map(len=rep(100, 4), n.mar=51, include.x=FALSE)
map2 <- sim.map(len=rep(100, 4), n.mar=51, include.x=FALSE)
mc <- mapcomp(map1, map2)
summary(mc)
plot(mc)