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Pull out a matrix of genotypes or genotype probabilities to use markers as covariates in QTL analysis.
formMarkerCovar(cross, markers, method=c("prob", "imp", "argmax"), ...)A matrix containing genotype probabilities or genotype indicators,
suitable for use as covariates in scanone.
An object of class cross. See
read.cross for details.
A vector of character strings of marker or pseudomarker
names. Pseudomarker names may be of the form "5@21.5" (for chr 5
at 21.5 cM), but then all names must be of this form.
If method="prob", the genotype probabilities from
calc.genoprob are used; otherwise we use
fill.geno to impute missing data, with this method.
Passed to fill.geno, if necessary.
Karl W Broman, broman@wisc.edu
pull.geno, pull.genoprob,
fill.geno, scanone
data(hyper)
hyper <- calc.genoprob(hyper, step=0)
peakMarker <- "D4Mit164"
X <- formMarkerCovar(hyper, peakMarker)
hyper <- hyper[c(1,4),]
out <- scanone(hyper, addcovar=X)
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