mergematrices {happy}R Documentation

Construct matrices used to merge together founder strains

Description

mergematrices() creates a list containing two matrices suitable for pre-multiplying with an additive or full happy marker design matrix, in order to produce matrices with certain columns combined. These reduced matrices are used to test whether the specified merge reduces the significance of the fit. This function is not usually called directly but is used by mergfit() and hfit() megedpositionmatrix() will return either the merged design matrix or the mergematrices object corresponding to an object returned by mergeprepare()

Usage

 mergematrices( strains, mergelist=NULL, verbose=FALSE )
 mergedpositionmatrix( h, position, prepmerge, model='additive',
verbose=FALSE, design=TRUE )

Arguments

strains character array of strain names
mergelist a list of lists of strains describing how the strains are grouped together. For instance mergelist <- list( A=list('AJ', 'BALB', 'AKR'), T=list('RIII','I', 'DBA', 'C57', 'C3H') ) divides the strains into two groups corresponding to the alleles A, T (the allele names are not important). It is essential that the all strain names match all the values in strains.
verbose switch to determine whether to tell what is happening.
h an object returned by a previous call to happy()
position the coordinate of the polymorphism to be tested, ie an entry in prepmerge$testmarkerdata$POSITION
prepmerge an object returned by mergeprepare()
model the type of model to be fitted - 'additive' or 'full'
design switch to make mergepositionmatrix return the mergematrix object rather than the merged design matrix

Value

mergematrices() and mergepositionmatrix() return an object comprising a list with two elements:

amat the matrix to apply to an additive-model design matrix
imat the matrix to apply to a full-model (interaction) design matrix

Author(s)

Richard Mott

See Also

happy(), mergefit(), hfit(), mergelist()


[Package happy version 2.1 Index]