sim.mpcross: Simulate data from multi-parent designs
In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description Usage Arguments Details Value Note See Also Examples

Data is simulated according to a pedigree, map and QTL model

sim.mpcross(map, pedigree, qtl = NULL, vare = 1, error.prob = 0,
  missing.prob = 0, full.prob = 0, keep.qtlgeno = TRUE,
  transpos = integer(0), transFounder = 0, map.function = c("haldane",
  "kosambi"), seed = 1, fg = NULL, founderld = FALSE)

`map`	Linkage map with which to generate data. See `sim.map`
`pedigree`	Pedigree for a multi-parent cross. Can be generated using `sim.mpped`
`qtl`	QTL model, defined by a matrix with one row per QTL and 6 columns: the chromosome of the QTL, the position in cM on that chromosome, and the four founder effects
`vare`	Phenotypic error variance
`error.prob`	Probability of genotyping errors - data will be changed with this probability to one of the other founder values
`missing.prob`	Probability of missing data in final genotypes
`full.prob`	Probability of fully informative markers. Markers will be assigned with this probability to retain IBD genotypes from founders rather than being recoded into binary values. See details below for more information
`keep.qtlgeno`	Flag for whether to retain the QTL genotypes as a component in the output `mpcross` object
`transpos`	Positions of potential translocation (vector)
`transFounder`	Which founder carries the translocation
`map.function`	Map function for conversion of linkage map into recombination fractions. Default is "haldane"
`seed`	Random seed for generation of data
`fg`	Input founder genotypes (optional) - otherwise generated randomly
`founderld`	Flag for whether to generate founder genotypes in linkage equilibrium (FALSE=default) or according to recombination map (TRUE)

Data are initially generated by transmitting founder genotypes down through the pedigree to the finals. Errors, missing data, and binary alleles are then overlaid on this data (stored in $ibd). If founderld==FALSE, binary alleles are generated at each locus with probability 0.25 that one founder will have the allele; 0.50 that two founders will have the allele; and 0.25 that three founders will have the allele. The founders with the allele are randomly selected after the number of founders with the allele has been simulated. If founderld==TRUE then some markers may be monomorphic and will need to be removed from the resulting object using clean.mpcross.

Note that if founder genotypes are input they should be coded as follows: DArT markers take values in 0,1 SNP markers take values in 0,2 All other markers take some other set of values.

Object of class mpcross. See mpcross for further details. Additional components are:

`ibd`	Fully informative founder genotypes for all markers
`qtlgeno`	If argument `keep.qtlgeno` is `TRUE` then QTL genotypes will be retained

Translocations can only be generated when founderld==FALSE and no founder genotypes are input. Note that founder effects in the QTL model are per allele; thus, the phenotypic difference between a line carrying the founder and one that is not will be twice the input founder effect (because all lines are inbred).

sim.mpped, sim.map

map <- qtl::sim.map(len=100, 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, 50, .4, 0, 0, 0), 
	nrow=1, ncol=6, byrow=TRUE), seed=1)