dlmap-internal: Internal dlmap functions
In dlmap: Detection Localization Mapping for QTL

Description Usage Details Author(s) References

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

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)

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/.

dlmap documentation built on May 2, 2019, 2:45 a.m.