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| baySeq-package | Empirical Bayesian analysis of patterns of differential expression in count data. |
| baySeq | Empirical Bayesian analysis of patterns of differential expression in count data. |
| baySeq-class | baySeq - classes |
| baySeq-classes | baySeq - classes |
| bimodalSep | A function that, given a numeric vector, finds the value which splits the data into two sets of minimal total variance. |
| CDPost | 'countData' object derived from data file 'simData' with estimated likelihoods of differential expression. |
| CDPriors | 'countData' object derived from data file 'simData' with estimated priors. |
| countData | baySeq - classes |
| countData-class | baySeq - classes |
| dim-method | baySeq - classes |
| getLibsizes | Estimates library scaling factors (library sizes) for count data. |
| getLikelihoods | Finds posterior likelihoods for each count as belonging to some hypothesis. |
| getLikelihoods.Dirichlet | Finds posterior likelihoods for each count as belonging to some hypothesis. |
| getLikelihoods.NB | Finds posterior likelihoods for each count as belonging to some hypothesis. |
| getLikelihoods.NBboot | Finds posterior likelihoods for each count as belonging to some hypothesis. |
| getLikelihoods.Pois | Finds posterior likelihoods for each count as belonging to some hypothesis. |
| getPosteriors | An internal function in the baySeq package for calculating posterior likelihoods given likelihoods of the data. |
| getPriors | Estimates prior parameters for the underlying distributions of 'count' data. |
| getPriors.Dirichlet | Estimates prior parameters for the underlying distributions of 'count' data. |
| getPriors.NB | Estimates prior parameters for the underlying distributions of 'count' data. |
| getPriors.Pois | Estimates prior parameters for the underlying distributions of 'count' data. |
| getTPs | Gets the number of true positives in the top n counts selected by ranked posterior likelihoods |
| groups | baySeq - classes |
| groups-method | baySeq - classes |
| groups<- | baySeq - classes |
| groups<--method | baySeq - classes |
| mobAnnotation | Annotation data for a set of small RNA loci derived from sequencing of grafts of Arabidopsis thaliana intended for differential expression analyses. |
| mobData | Data from a set of small RNA sequencing experiments carried out on grafts of Arabidopsis thaliana intended for differential expression analyses. |
| plotMA.CD | 'MA'-plot for count data. |
| plotPosteriors | Plots the posterior likelihoods estimated for a 'countData' object against the log-ratios observed between two sets of sample data. |
| plotPriors | Plots the density of the log values estimated for the mean rate in the prior data for the Negative Binomial approach to detecting differential expression |
| rbind | baySeq - classes |
| rbind-method | baySeq - classes |
| replicates | baySeq - classes |
| replicates-method | baySeq - classes |
| replicates<- | baySeq - classes |
| replicates<--method | baySeq - classes |
| show-method | baySeq - classes |
| simData | Simulated data for testing the baySeq package methods; simulated counts and library sizes from a pairwise differential expression analysis. |
| topCounts | Get the top counts corresponding to some group from a 'countData' object |
| [-method | baySeq - classes |