mpMap (version 1.14)

clean.mpcross: Check data format and compute summary statistics for genotypes

Description

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.

Usage

"clean" (object, ...)

Arguments

object

Object of class mpcross

...

Additional arguments

Value

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

Details

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.

See Also

mpcross

Examples

map <- 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 <- clean(sim.dat)