copynumberAccessors: Accessors for allele-specific or total copy number

In crlmm: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

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)

crlmm documentation built on Nov. 8, 2020, 4:55 p.m.