max.scantwo {qtl} | R Documentation |
Print the pair of loci with the largest LOD score in the results of
scantwo
.
## S3 method for class 'scantwo': max(object, lodcolumn=1, what=c("best", "full", "add", "int"), df=FALSE, na.rm=TRUE, ...)
object |
An object of class scantwo , the output of the
function scantwo . |
lodcolumn |
If the scantwo results contain LOD scores for multiple phenotypes, this argument indicates which to use. |
what |
Indicates for which LOD score the maximum should be reported. |
df |
If TRUE, the degrees of freedom associated with the LOD scores are shown. |
na.rm |
Ignored. |
... |
Ignored. |
This is very similar to the summary.scantwo
function, though this pulls out one pair of positions.
If what="best"
, we find the pair of positions at which the LOD
score for the full model (2 QTL + interaction) is maximized, and then
also print the positions on that same pair of chromosomes at which the
additive LOD score is maximized.
In the other cases, we pull out the pair of positions with the largest
LOD score; which LOD score is considered is indicated by the
what
argument.
An object of class summary.scantwo
, to be printed by
print.summary.scantwo
, with the pair of positions with the
maximum LOD score. (Which LOD score is considered is indicated by the
what
argument.)
Karl W Broman, kbroman@biostat.wisc.edu
scantwo
, plot.scantwo
,
summary.scantwo
data(fake.f2) fake.f2 <- calc.genoprob(fake.f2, step=10) out.2dim <- scantwo(fake.f2, method="hk") max(out.2dim)