makeCgh {QDNAseq} | R Documentation

## 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.

### Author(s)

Ilari Scheinin

### Examples

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

[Package QDNAseq version 1.16.0 Index]