R: Plot grid of error LOD values

plotErrorlod {qtl} | R Documentation

## Plot grid of error LOD values

### Description

Plot a grid of the LOD scores indicating which genotypes are likely to be in error.

### Usage

    plotErrorlod(x, chr, ind, breaks=c(-Inf,2,3,4.5,Inf),
                  col=c("white","gray85","hotpink","purple3"),
                  alternate.chrid=FALSE, ...)

### Arguments

`x` | An object of class `cross`. See `read.cross` for details.
`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 `-` to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.
`ind` | Indicates the individuals for which the error LOD scores should be plotted (passed to `subset.cross`).
`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.

### Details

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.

### Value

None.

### Author(s)

Karl W Broman, broman@wisc.edu

### References

Lincoln, S. E. and Lander, E. S. (1992) Systematic detection of errors in genetic linkage data. Genomics 14, 604–610.

### See Also

`calc.errorlod`, `top.errorlod`, `image`, `subset.cross`, `plotGeno`

### Examples

    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)

[Package qtl version 1.46-2 Index]