Pull out recombination fractions or LOD scores from a cross object
Pull out either the pairwise recombination fractions or the LOD
scores, as calculated by est.rf, from a cross object.
pull.rf(cross, what=c("rf", "lod"), chr)cross |
An object of class |
what |
Indicates whether to pull out a matrix of estimated recombination fractions or a matrix of LOD scores. |
chr |
Optional vector indicating the chromosomes to consider.
This should be a vector of character strings referring to chromosomes
by name; numeric values are converted to strings. Refer to
chromosomes with a preceding |
An object of class "rfmatrix", which is a matrix of either
estimated recombination fractions between all marker pairs or of LOD
scores (for the test of rf=1/2) for all marker pairs.
The genetic map is included as an attribute.
Karl W Broman, broman@wisc.edu
data(fake.f2) fake.f2 <- est.rf(fake.f2) rf <- pull.rf(fake.f2) lod <- pull.rf(fake.f2, "lod") plot(rf[1,], lod[1,], xlab="rec frac", ylab="LOD score") marker <- markernames(fake.f2, chr=5)[6] par(mfrow=c(2,1)) plot(rf, marker, bandcol="gray70") plot(lod, marker, bandcol="gray70")
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.