Description Usage Arguments Details Author(s)

Calculates the total distance between observed peaks and (closest) expected peaks, with added penalty to force a specific copy number configuration to one of the peak. Not meant to be called directly.

1 2 |

`selectedPeaks` |
Passed from peakProximity |

`S` |
The S parameter |

`t` |
The t parameter (sums to 1). |

`wd` |
Weights given to each point in a cluster of points |

`xonly` |
Ignore the y-axis, only calculate distance based on the x-axis |

`weightbydiff` |
Ignore, not extensively tested. |

`weightbyarp` |
Ignore, not extensively tested. |

`penaltymultiplier` |
If a peak (a line of selectedPeak) is to be forced to represent a particular copy number configuration, then the fit is forced by adding a penalty multiplier to the distance between that peak and the expected location of the copy number configuration. |

`penaltymultipliery` |
If the penalty multiplier is to differ in the x- and y- directions, then use this as an additional multiplier in the y- direction (the penalty multiplier in the y-direction is then penaltymultiplier*penaltymultipliery). |

`...` |
Arguments passed to prepAR (ie, preserveMatPatDiff) |

To force a peak, a third column ($w) in selectedPeak is needed. That column contains a single non-zero integer value taking the format xy (for a 2-subclone model), where x is the copy number in the first sub-clone, y in the second subclone. In a 3-subclone system, the format is xyz, etc. All integers x,y,z,etc must take non-negative values no larger than 9.

Mathieu Lemire

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.