abcdDNA {Repitools} | R Documentation |
This function performs differential analyses, given a QdnaData
object with the sample-specific offsets already calculated (i.e. call getSampleOffsets
before calling abcdDNA
), a coefficient (or set of coefficients) to test and dispersion(s). In essence, the function is a wrapper for constructing the offset matrix, fitting the generalized linear model and performing a likelihood ratio test.
abcdDNA(obj, coef = ncol(obj$design), dispersion = NULL)
obj |
a |
coef |
coefficient (or coefficients) of the design matrix to test |
dispersion |
estimate(s) of dispersion to use for negative binomial testing |
This function is simply a wrapper for taking the details in an QdnaData
object and perform the differential analyses, adjusting for copy number if specified.
a DGEGLM
(see the edgeR package) containing the results of the differential comparison
Mark Robinson
http://imlspenticton.uzh.ch/robinson_lab/ABCD-DNA/ABCD-DNA.html
# library(Repitools) # qd <- QdnaData(counts=counts, regions=gb, design=design, # cnv.offsets=cn, neutral=(regs=="L=4 P=2")) # qd <- getSampleOffsets(qd,ref=1) # plotQdnaByCN(qd,cnv.group=regs,idx.ref=3,idx.sam=2) # f <- abcdDNA(qd, dispersion=.05, coef=2) # topTags(f)