Description Usage Arguments Details Value Author(s) References See Also Examples
Plot a grid of the LOD scores indicating which genotypes are likely to be in error.
1 2 3 |
x |
An object of class |
chr |
Optional vector indicating the chromosomes to be drawn in
the plot. 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 |
ind |
Indicates the individuals for which the error LOD scores
should be plotted (passed to |
breaks |
A set of breakpoints for the colors; must give one more breakpoint than color. Intervals are open on the left and closed on the right, except for the lowest interval. |
col |
A vector of colors to appear in the image. |
alternate.chrid |
If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished. |
... |
Ignored at this point. |
Uses image
to plot a grid with different shades
of pixels to indicate which genotypes are likely to be in error.
Darker pixels have higher error LOD scores: LOD ≤ 2 in white; 2 < LOD <= 3 in gray; 3 < LOD <= 4.5 in pink; LOD > 4.5 in purple.
None.
Karl W Broman, kbroman@biostat.wisc.edu
Lincoln, S. E. and Lander, E. S. (1992) Systematic detection of errors in genetic linkage data. Genomics 14, 604–610.
calc.errorlod
,
top.errorlod
, image
,
subset.cross
, plotGeno
1 2 3 4 5 6 7 8 | data(hyper)
# Calculate error LOD scores
hyper <- calc.errorlod(hyper,error.prob=0.01)
# plot the error LOD scores; print those above a specified cutoff
plotErrorlod(hyper)
plotErrorlod(hyper,chr=1)
|
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