discontPlot {CAFE} | R Documentation

## Plot with discontinuous smoother

### Description

Plots chromosome plots with a discontinuous smoother

### Usage

    discontPlot(datalist,samples=c(1,2),chromNum=1,gamma=300,idiogram=FALSE,
    file="default")

### Arguments

`datalist` | The CAFE datalist to be analyzed, i.e. the output of `ProcessCels`.
`samples` | A vector or sample numbers to be plotted
`chromNum` | the chromosome to be plotted
`gamma` | The `gamma` level can be roughly compared to the sliding window size in a normal continuous smoother. The `gamma` level determines how strict the algorithm functions; a higher level will correspond to fewer jumps. This can not be higher than the total number of probesets on the to-be-analyzed chromosome. Must be a positive integer.
`idiogram` | if `TRUE`, will overlay a chromosome idiogram over the chromosome plot
`file` | Specify a file name to store output png file

### Value

Plot to file system; Returns a ggplot2 graph if `chromNum!="ALL"`. When `chromNum=="ALL"`, returns a list of ggplot2 graphs.

### Author(s)

Sander Bollen

### References

Friedrich, F., Kempe, a, Liebscher, V., & Winkler, G. (2008). Complexity Penalized M-Estimation. Journal of Computational and Graphical Statistics, 17(1), 201-224. doi:10.1198/106186008X285591

### See Also

`rawPlot` `slidPlot` `facetPlot`

### Examples

    data("CAFE_data")
    discontPlot(CAFE_data,samples=9,chromNum=17,gamma=300)

[Package CAFE version 1.23.0 Index]