abcdDNA {Repitools} | R Documentation

## A wrapper for fitting the offset-adjusted ABCD-DNA GLM

### Description

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.

### Usage

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

### Arguments

`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

### Details

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.

### Value

a `DGEGLM` (see the edgeR package) containing the results of the differential comparison

### Author(s)

Mark Robinson

### References

http://imlspenticton.uzh.ch/robinson_lab/ABCD-DNA/ABCD-DNA.html

### See Also

`QdnaData`,

### Examples

    # 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)

[Package Repitools version 1.33.3 Index]