Description Usage Arguments Value Parallel processing Author(s) See Also Examples

Segments normalized copy number data.

1 2 | ```
segmentBins(object, smoothBy=FALSE, alpha=1e-10, undo.splits="sdundo", undo.SD=1,
force=FALSE, transformFun="log2", ...)
``` |

`object` |
An object of class QDNAseqCopyNumbers. |

`smoothBy` |
An optional integer value to perform smoothing before
segmentation by taking the mean of every smoothBy bins, and then
segment those means. Default ( |

`alpha` |
Significance levels for the test to accept change-points. Default is 1e-10. |

`undo.splits` |
A character string specifying how change-points are to be undone, if at all. Default is "sdundo", which undoes splits that are not at least this many SDs apart. Other choices are "prune", which uses a sum of squares criterion, and "none". |

`undo.SD` |
The number of SDs between means to keep a split if undo.splits="sdundo". Default is 1.0. |

`force` |
Whether to force execution when it causes removal of downstream calling results. |

`transformFun` |
A function to transform the data with. This can be
the default "log2" for log2(x + .Machine$double.xmin),
"sqrt" for the Anscombe transform of sqrt(x * 3/8) which
stabilizes the variance, "none" for no transformation, or any
R function that performs the desired transformation and also its
inverse when called with parameter |

`...` |
Additional arguments passed to |

Returns an object of class QDNAseqCopyNumbers with segmentation results added.

This function uses future to segment samples in parallel.

Ilari Scheinin

Internally, `segment`

of the DNAcopy package,
which implements the CBS method, is used to segment the data.

1 2 3 4 5 6 7 8 9 | ```
data(LGG150)
readCounts <- LGG150
readCountsFiltered <- applyFilters(readCounts)
readCountsFiltered <- estimateCorrection(readCountsFiltered)
copyNumbers <- correctBins(readCountsFiltered)
copyNumbersNormalized <- normalizeBins(copyNumbers)
copyNumbersSmooth <- smoothOutlierBins(copyNumbersNormalized)
copyNumbersSegmented <- segmentBins(copyNumbersSmooth)
``` |

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