Description Usage Details Author(s) References
Internal dlmap functions. These are generally not to be called by the user.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | dlcross.cross(genobj, pheobj, idname, step, fixpos, estmap)
dlcross.dlmap(genobj, pheobj, mapobj, idname, genfile, mapfile, phefile, type, step, fixpos, estmap, ...)
dlcross.other(genobj, pheobj, mapobj, idname, genfile, mapfile, phefile)
dldetect(input, algorithm, filestem, ...)
dllocalize(input, algorithm, QTLperChr, ...)
dlmapdet(input, algorithm, s.chr, chrSet, prevLoc = NULL, ...)
dlmaploc(input, algorithm, s.chr, chrSet, prevLoc = NULL, ...)
dltest(input, algorithm, chrSet, prevLoc = NULL, ...)
calcpos(cross, step, fixpos)
calc.genoprob2(cross, pos, error.prob=1e-04, map.function=c("haldane", "kosambi", "c-f", "morgan"))
waldtest.asreml(object, cc)
cintern(cc, tau, vrb, sigma2)
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The detect, localize, test and mapping functions form the basis of the
DLMapping algorithm. The argument algorithm
allows for versions using
either lme
or asreml
to fit 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.
calc.genoprob2 is a modification of a function from the R/qtl package to allow for calculation of genotype probabilities at more general positions than a fixed step size.
Emma Huang and Andrew George
Huang, B.E. and George, A.W. 2009. Look before you leap: A New Approach to QTL Mapping. TAG 119:899-911
Broman et al. (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890
B. Emma Huang, Rohan Shah, Andrew W. George (2012). dlmap: An R Package for Mixed Model QTL and Association Analysis. Journal of Statistical Software 50(6): 1-22. URL http://www.jstatsoft.org/v50/i06/.
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