clean.mpcross: Check data format and compute summary statistics for...
In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description Usage Arguments Details Value See Also Examples

Given an object of class 'mpcross', the function checks that the data is in the correct format, containing founder and final genotypes, ids, and a pedigree. The number of markers genotyped for both founders and finals should coincide. The pedigree should be completely numeric. Markers which are not polymorphic across the founders are removed, as are markers which have missing values in the founders.

1 2	## S3 method for class 'mpcross' clean(object, ...)

`object`	Object of class `mpcross`
`...`	Additional arguments

Summary statistics for the genotypes are printed, included the number of markers with varying levels of missing data, with varying levels of segregation distortion, and with different numbers of alleles.

`drop1`	List of markers which are monomorphic in founders
`drop2`	List of markers which have missing values in founders
`drop3`	List of markers with alleles appearing in finals but not founders
`alleles`	Number of alleles at each marker
`missing`	Percent missing data at each marker
`seg`	Matrix with one row for each marker and columns for the marker name, the chisquare test for segregation distortion, and the p-value of the test

mpcross

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, 45, .4, 0, 0, 0), 
	nrow=1, ncol=6, byrow=TRUE),seed=1)
dat.chk <- qtl::clean(sim.dat)