QDNAseq (version 1.8.0)

makeCgh: Constructs a 'cghRaw', 'cghSeg', or 'cghCall' object

Description

Constructs a 'cghRaw', 'cghSeg', or 'cghCall' object.

Usage

makeCgh(object, filter=TRUE, chromosomeReplacements=c(X = 23, Y = 24, MT = 25), ...)

Arguments

object

A QDNAseqCopyNumbers object.

filter

If TRUE, bins are filtered, otherwise not.

chromosomeReplacements

A named integer vector of chromosome name replacements to be done. QDNAseq stores chromosome names as characters, but CGHcall expects them to be integers. Defaults to c(X=23, Y=24, MT=25) for human. Value of "auto" will use running numbers in order of appearance in the bin annotations.

...

Not used.

Value

Returns a cghRaw if the object has not been segmented, a cghSeg if it has been segmented but not called, or cghCall if it has been called as well.

Examples

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