QDNAseq (version 1.8.0)

segmentBins: Segments normalized copy number data

Description

Segments normalized copy number data.

Usage

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

Arguments

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 (FALSE) is to perform no smoothing. smoothBy=1L is a special case that will not perform smoothing, but will split the segmentation process by chromosome instead of by sample. This has an effect when using parallel computing or specifying seeds for random number generation.

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 inv=TRUE.

seeds

An optional integer vector of seeds for random number generation, recycled as needed. Normally, the segmentation process is split by sample, and provided seeds also used per sample. But when smoothing is performed (or in the the special case of smoothBy=1L), the process is split by chromosome, seeds used per chromosome, and results not necessarily reproducible across samples.

...

Additional arguments passed to segment.

Value

Returns an object of class QDNAseqCopyNumbers with segmentation results added.

See Also

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

Examples

data(LGG150)
readCounts <- LGG150
readCountsFiltered <- applyFilters(readCounts)
readCountsFiltered <- estimateCorrection(readCountsFiltered)
copyNumbers <- correctBins(readCountsFiltered)
copyNumbersNormalized <- normalizeBins(copyNumbers)
copyNumbersSmooth <- smoothOutlierBins(copyNumbersNormalized)
copyNumbersSegmented <- segmentBins(copyNumbersSmooth)