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

View source: R/commonCondLogLikDerDelta.R

Common conditional log-likelihood parameterized in terms of delta (`phi / (phi+1)`

)

1 | ```
commonCondLogLikDerDelta(y, delta, der = 0)
``` |

`y` |
list with elements comprising the matrices of count data (or pseudocounts) for the different groups |

`delta` |
delta ( |

`der` |
derivative, either 0 (the function), 1 (first derivative) or 2 (second derivative) |

The common conditional log-likelihood is constructed by summing over all of the individual genewise conditional log-likelihoods. The common conditional log-likelihood is taken as a function of the dispersion parameter (`phi`

), and here parameterized in terms of delta (`phi / (phi+1)`

). The value of delta that maximizes the common conditional log-likelihood is converted back to the `phi`

scale, and this value is the estimate of the common dispersion parameter used by all genes.

numeric scalar of function/derivative evaluated at given delta

Davis McCarthy

`estimateCommonDisp`

is the user-level function for estimating the common dispersion parameter.

1 2 3 4 5 | ```
counts<-matrix(rnbinom(20,size=1,mu=10),nrow=5)
d<-DGEList(counts=counts,group=rep(1:2,each=2),lib.size=rep(c(1000:1001),2))
y<-splitIntoGroups(d)
ll1<-commonCondLogLikDerDelta(y,delta=0.5,der=0)
ll2<-commonCondLogLikDerDelta(y,delta=0.5,der=1)
``` |

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