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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 or paired count as belonging to some model. |
| getLikelihoods.BB | Finds posterior likelihoods for each count or paired count as belonging to some model. |
| getLikelihoods.NB | Finds posterior likelihoods for each count or paired count as belonging to some model. |
| 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.BB | Estimates prior parameters for the underlying distributions of 'count' data. |
| getPriors.NB | 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 |
| libsizes | baySeq - classes |
| libsizes-method | baySeq - classes |
| libsizes<- | baySeq - classes |
| libsizes<--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. |
| pairData | Simulated data for testing the baySeq package methods for paired data |
| pairedData | baySeq - classes |
| pairedData-class | baySeq - classes |
| 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 |
| topCounts | Get the top counts corresponding to some group from a 'countData' object |
| [-method | baySeq - classes |