mpcross: Multi-parent cross object

In mpMap: Multi-parent RIL genetic analysis

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)

mpMap documentation built on May 29, 2017, 2:50 p.m.