| max.scanone {qtl} | R Documentation |
Print the row of the output from scanone that
corresponds to the maximum LOD, genome-wide.
## S3 method for class 'scanone': max(object, chr, lodcolumn=1, df=FALSE, na.rm=TRUE, ...)
object |
An object of the form output by the function
scanone: a data.frame whose third column is the
LOD score. |
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 - to have all chromosomes but
those considered. A logical (TRUE/FALSE) vector may also be used. |
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
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)