QL.results: Obtain p-values and q-values using results from 'QL.fit'
In gitlongor/QuasiSeq: Analyzing RNA Sequencing Count Tables Using Quasi-Likelihood

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

Obtain significance results for quasi-likelihood model fits to RNA-seq expression count data using the methods detailed in Lund, Nettleton, McCarthy, and Smyth (2012).

1 2	QL.results(fit,Dispersion="Deviance",spline.df=NULL,Plot=TRUE)

`fit`	The list returned by the function QL.fit
`Dispersion`	Must be one of "Deviance" or "Pearson", specifying which type of estimator should be used for estimating quasi-likelihood dispersion parameter.
`spline.df`	Optional. User may specify the degrees of freedom to use when fitting a cubic spline to log-scale(estimated dispersion) versus the log(average count). Default uses cross-validation in `sreg` function to pick appropriate degrees of freedom.
`Plot`	logical. If TRUE, the estimated dispersion versus the average count are plotted on a log-scale with the corresponding cubic spline fit overlaid.

list containing:

`"P.values"`	list of matrices providing p-values for the QL, QLShrink and QLSpline methods, respectively. The i^th column of each element of `pvals` corresponds to the hypothesis test assigned in the i^th row of `test.mat`.
`"Q.values"`	list of matrices providing q-values for the QL, QLShrink and QLSpline methods, respectively. The i^th column of each element of `qvals` corresponds to the hypothesis test assigned in the i^th row of `test.mat`. Q-values are computed using the methods of Nettleton et al. (2006) JABES 11, 337-356.
`"F.stat"`	list of matrices providing F-statistics for the QL, QLShrink and QLSpline methods, respectively. The i^th column of each element of `F.stat` corresponds to the hypothesis test assigned in the i^th row of `test.mat`.
`"m0"`	matrix providing estimated number of true null hypotheses for each test(arranged by row) under each of the three methods(arranged by column). `m0` values are computed using the methods of Nettleton et al. (2006) JABES 11, 337-356.
`"d0"`	vector containing estimated additional denominator degrees of freedom gained from shrinking dispersion estimates in the QLShrink and QLSpline procedures, respectively.

Steve Lund lundsp@gmail.com

Lund, Nettleton, McCarthy and Smyth (2012) "Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates" SAGMB, 11(5).

QL.fit, NBDev, mockRNASeqData