dlmap-internal {dlmap}R Documentation

Internal dlmap functions

Description

Internal dlmap functions. These are generally not to be called by the user.

Usage

dlmap.detect.asreml(input, filestem, ...)
dlmap.detect.lme(input, filestem)

dlmap.localize.asreml(input, QTLperChr, ...)
dlmap.localize.lme(input, QTLperChr)

dlmap.map.det.asreml(input, s.chr, chrSet, prevLoc = NULL, ...)
dlmap.map.det.lme(input, s.chr, chrSet, prevLoc = NULL)

dlmap.map.loc.asreml(input, s.chr, chrSet, prevLoc = NULL, ...)
dlmap.map.loc.lme(input, s.chr, chrSet, prevLoc = NULL)

dlmap.test.asreml(input, chrSet, prevLoc = NULL, ...)
dlmap.test.lme(input, chrSet, prevLoc = NULL)

dlmap.merge(genCross, envData=NULL, step, fixpos, nperm, alpha, pindex=1, phename, idname, estmap=TRUE)

dlmap.read(genfile, phefile, mapfile, phename, filestem)

dlmap.calc.pos(exp.dat, step, fixpos)

Details

The detect, localize, test and mapping functions form the basis of the DLMapping algorithm. There are versions for each version of dlmap (making use of either lme or asreml to fit the mixed models).

The merge function is used to combine the genotype and environmental data, and also imputes missing values in the genotype data according to the Viterbi algorithm. See fill.geno for more details. Note that individuals with no phenotypic response data are omitted in the merged dataset. Individuals with phenotypic but no genotypic data are retained, but the genotypes are not imputed.

Author(s)

Emma Huang and Andrew George

References

Huang, B.E. and George, A.W. Look before you leap: A New Approach to QTL Mapping (in preparation)


[Package dlmap version 1.0 Index]