abcdDNA: A wrapper for fitting the offset-adjusted ABCD-DNA GLM
In Repitools: Epigenomic tools

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1	abcdDNA(obj, coef = ncol(obj$design), dispersion = NULL)

`obj`	a `QdnaData` object
`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

QdnaData,

# 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)