mpMap (version 1.14)

mpcross: Multi-parent cross object

Description

The class of object generated from sim.mpcross and the format input to functions to construct linkage maps for multi-parent crosses. Basic constructor - takes required R objects and formats as an mpcross object.

Usage

mpcross(founders, finals, pedigree, id, fid)

Arguments

founders

Matrix of founder genotypes

finals

Matrix of final genotypes

pedigree

Cross pedigree

id

Vector of numeric IDs for lines (which rows in pedigree are observed)

fid

Vector of founder IDs

Value

Let n.founders be the number of founders (either 4 or 8); n.finals be the number of final RILs genotyped; and n.mrk be the number of markers genotyped. Then

founders

Founder genotypes - a matrix with dimensions n.founders x n.mrk. Row names of the matrix should be lines names; Column names should be marker names

finals

Final genotypes - a matrix with dimensions n.finals x n.mrk. Row names of the matrix should be line name; column names should be marker names.

id

Vector of final IDs with length n.finals

fid

Vector of founder IDs with length n.founders

pedigree

Numeric pedigree with 3 columns - mother, father, ID

pheno

Phenotypic data

Optional components:

map

Linkage map - either from which data was generated in sim.mpcross or estimated at some point

ibd

IBD genotypes from founders if data has been generated from sim.mpcross

qtlgeno

Genotypes at QTL if data has been generated from sim.mpcross

rf

Recombination fractions if data has been analyzed with mpestrf

lg

Linkage groups if data has been analyzed with mpgroup

See Also

sim.mpcross, mpestrf, mpgroup

Examples

map <- sim.map(len=rep(100,2), n.mar=11, eq.spacing=TRUE, include.x=FALSE)
sim.ped <- sim.mpped(4, 1, 500, 6, 1)
sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow=TRUE), seed=1)