crlmm (version 1.30.0)

copynumberAccessors:

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.

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.

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.

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)