hdesign {happy}R Documentation

Extract design matrix or genotypes for a specific marker interval from a happy object

Description

hdesign() will call C to extract the design matrix to fit a QTL to a marker interval. hprob() will call C to extract a raw probability matrix. hgenotype() will return the raw genotype data for a marker

Usage

hdesign( h, marker, model='additive', mergematrix=NULL )
hprob( h, marker=NULL )
hgenotype ( h, marker, collapse=FALSE, sep="" )

Arguments

h an object returned by a previous call to happy()
marker either a character string giving the name of the marker or the index of the marker in the array h$markers
model either 'additive' (default) or 'full'. The additive design matrix returns an array with S columns, where S is the number of founder strains in the HS. The full design matrix returns a matrix with S(S-1)/2 columns, one for each combination of strains
mergematrix an object returned by mergematrices, used to define sets of strains that are to be merged together. This is accomplished by adding the corresponding columns in the original design matrix.
collapse a boolean variable indicating whether to collapse the alleles into a single genotype.
sep the text to be used to separate the alleles if collapsed.

Value

hdesign() returns a design matrix d[i,j], in which the ith row corresponds to the subject i, and the jth column to the corresponding strain or combination of strains or merged strains. hprob() returns a matrix i th row corresponds to the subject i, and the x=s*S+t th column contains the probability that the ancestral strains are s,t where S is the total number of strains. hgenotype() returns a Nx2 matrix i th row corresponds to the subject i, and column 1 contains the first allele and column 2 the second allele at the marker specified, or (if collapse=TRUE) a vector of genotypes with the alleles pasted together.

Author(s)

Richard Mott

See Also

happy(), hfit()

Examples

## Not run: h <- happy( 'HS.data', 'HS.alleles', generations=200 )
## Not run: d <- hdesign( h, 1 ) ## the first marker interval
## Not run: d <- hdesign( h, 'D1MIT264') ## the marker interval with left-hand marker D1MIT264
## Not run: d <- hdesign( h, 'D1MIT264', model='full' ) ## ditto with full design matrix

[Package happy version 2.1 Index]