Description Usage Arguments Value Author(s) See Also Examples
Print the row of the output from scanone
that
corresponds to the maximum LOD, genome-wide.
1 2 |
object |
An object of the form output by the function
|
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 |
lodcolumn |
An integer, indicating which of the LOD score columns should be considered in pulling out the peak (these are indexed 1, 2, ...). |
df |
If TRUE, the degrees of freedom associated with the LOD scores are shown. |
na.rm |
A logical indicating whether missing values should be removed. |
... |
Ignored. |
An object of class summary.scanone
, to be printed by
print.summary.scanone
. This is a data.frame with one row,
corresponding to the maximum LOD peak either genome-wide or for the
particular chromosome specified.
Karl W Broman, kbroman@biostat.wisc.edu
scanone
, plot.scanone
,
summary.scanone
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | data(listeria)
listeria <- calc.genoprob(listeria, step=2.5)
out <- scanone(listeria, model="2part", upper=TRUE)
# Maximum peak for LOD(p,mu)
max(out)
# Maximum peak for LOD(p,mu) on chr 5
max(out,chr=5)
# Maximum peak for LOD(p,mu) on chromosomes other than chr 13
max(out,chr="-13")
# Maximum peak for LOD(p)
max(out, lodcolumn=2)
# Maximum peak for LOD(mu)
max(out, lodcolumn=3)
|
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