| replacemap.scantwo {qtl} | R Documentation |
Replace the positions of LOD scores in output from
scantwo with values
based on an alternative map (such as a physical map), with
pseudomarker locations determined by linear interpolation.
## S3 method for class 'scantwo': replacemap(object, map)
object |
An object of class "scantwo", as output by the
function scantwo. |
map |
A list containing the alternative genetic map. All
chromosomes in object should have corresponding chromosomes in
map, and markers must be in the same order in the two maps.
There must be at least two markers on each chromosome in map
that appear in object. |
The positions of pseudomarkers are determined by linear interpolation
between markers. In the case of pseudomarkers beyond the ends of the
terminal markers on chromosomes, we use the overall lengths of the
chromosome in object and map to determine the new
spacing.
The input object with the positions of LOD scores
revised to match those in the input map.
Karl W Broman, kbroman@biostat.wisc.edu
replacemap.cross,
est.map, replacemap.scanone
data(hyper) origmap <- pull.map(hyper) newmap <- est.map(hyper) hyper <- replacemap(hyper, newmap) hyper <- calc.genoprob(hyper, step=0) out <- scantwo(hyper, method="hk") out.rev <- replacemap(out, origmap)