copynumberAccessors {crlmm} | R Documentation

## Accessors for allele-specific or total copy number

### Description

These methods can be applied after an object of class `CNSet` has been generated by the `crlmmCopynumber` function.

### Usage

    CA(object, ...)
    CB(object, ...)
    nuA(object)
    nuB(object)
    phiA(object)
    phiB(object)
    totalCopynumber(object,...)
    rawCopynumber(object,...)

### Arguments

`object` | An object of class `CNSet`.
`...` | An additional argument named 'i' can be passed to subset the markers and an argument 'j' can be passed to subset the samples. Other arguments are ignored.

### Details

At polymorphic markers, nuA and nuB provide the intercept coefficient (the estimated background intensity) for the A and B alleles, respectively. phiA and phiB provide the slope coefficients for the A and B alleles, respectively.

At nonpolymorphic markers, nuB and phiB are 'NA'.

These functions can be used to tranlate the normalized intensities to the copy number scale. Plotting the copy number estimates as a function of physical position can be used to guide downstream algorithms that smooth, as well as to assess possible mosaicism.

### Value

nu[A/B] and phi[A/B] return matrices of the intercept and slope coefficients, respectively.

CA and CB return matrices of allele-specific copy number.

totalCopynumber (or rawCopynumber) returns a matrix of CA+CB.

### Note

Subsetting the `CNSet` object before extracting copy number can be very inefficient when the data set is very large, particularly if using ff objects. The `[` method will subset all of the assay data elements and all of the elements in the LinearModelParameter slot.

### See Also

`crlmmCopynumber`, `CNSet-class`

### Examples

    ## Not run:
    data(cnSetExample)
    all(isCurrent(cnSetExample)) ## is the cnSet object current?

    ## --------------------------------------------------
    ## calculating allele-specific copy number
    ## --------------------------------------------------
    ## copy number for allele A, first 5 markers, first 2 samples
    (ca <- CA(cnSetExample, i=1:5, j=1:2))
    ## copy number for allele B, first 5 markers, first 2 samples
    (cb <- CB(cnSetExample, i=1:5, j=1:2))
    ## total copy number for first 5 markers, first 2 samples
    (cn1 <- ca+cb)

    ## total copy number at first 5 nonpolymorphic loci
    index <- which(!isSnp(cnSetExample))[1:5]
    cn2 <- CA(cnSetExample, i=index, j=1:2)
    ## note, cb is NA at nonpolymorphic loci
    (cb <- CB(cnSetExample, i=index, j=1:2))
    ## note, ca+cb will give NAs at nonpolymorphic loci
    CA(cnSetExample, i=index, j=1:2) + cb
    ## A shortcut for total copy number
    cn3 <- totalCopynumber(cnSetExample, i=1:5, j=1:2)
    all.equal(cn3, cn1)
    cn4 <- totalCopynumber(cnSetExample, i=index, j=1:2)
    all.equal(cn4, cn2)

    ## markers 1-5, all samples
    cn5 <- totalCopynumber(cnSetExample, i=1:5)
    ## all markers, samples 1-5
    cn6 <- totalCopynumber(cnSetExample, j=1:2)

    ## End(Not run)

[Package crlmm version 1.52.0 Index]