makeCgh: Constructs a 'cghRaw', 'cghSeg', or 'cghCall' object
In QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

Description Usage Arguments Value Author(s) Examples

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

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

`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.

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.

Ilari Scheinin

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

38,819	total bins
38,819	of which in selected chromosomes
36,722	of which with reference sequence
33,347	final bins
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
Applying median normalization ...
Smoothing outliers ...