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 |

`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

1 2 3 4 5 6 7 | ```
# 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)
``` |

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