copynumberAccessors {crlmm} | R Documentation |
These methods can be applied after an object of class CNSet
has
been generated by the crlmmCopynumber
function.
CA(object, ...) CB(object, ...) nuA(object) nuB(object) phiA(object) phiB(object) totalCopynumber(object,...) rawCopynumber(object,...)
object |
An object of class |
... |
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. |
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.
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.
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.
## 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)