Man pages for adamsardar/metaDEGth
Combining differential expression P-values in a statistically consistent fashion whilst respecting background signal/noise trends
| BetaUniformModel-class | Object representation of a beta-uniform model fit to a... |
| betaUniformPvalueSumTest | A meta-analysis P-value summarising a set of hypotheses |
| betaUniformScore | For each P-value, compute the log likelihood ratio of... |
| bioplanetPathwaysDT | Bioplanet - catalogue of biological pathways |
| cas9OCT4_hsZygote_diffexDT | Differential expression from RNAseq assay of OCT4(POU5F1)... |
| constructHyperexponentialSumTransitionMatrix | Model a sum of log-transformed beta-uniform mixture draws as... |
| convertFromBUM | A simple adapter from the class produced by BioNet |
| dbetauniform | Density function for Beta-uniform Model |
| erlotinib_adrHCC827_diffexDT | Microarray assay to understand acquired drug resistance to... |
| falseNegativeFraction | False negative rate from M&P: B table 1 and equation 5 |
| falsePositiveFraction | FALSE positive rate from M&P: C table 1 and equation 5 |
| FDRestimate | False discovery rate - of BH fame. Equation 6 from M&P |
| fishersPvalueSumTest | Combine multiple independent P-values together using Fisher's... |
| fitBetaUniformMixtureDistribution | Fit a Beta-Uniform decomposition model to the provided... |
| hsPathBankProteinSets_DT | Pathbank - catalogue of biological pathways |
| koATF3_HCT116_diffexDT | Differential expression from microarray assay of ATF3... |
| metaDEG | meta differential gene expression (DEG) analysis |
| metaDEGth | metaDEGth: an enrichment analysis method for differential... |
| metaDEGth-package | Combining differential expression P-values in a statistically... |
| noiseFractionUpperBound | Upper bound on the the noise component of mixture... |
| plot.BetaUniformModel | Plot summary for fitted Beta-Uniform models |
| pValueThresholdAtConfidence | pValueThreshold estimate - estimates a threshdold such that... |
| qbetauniform | Quantile function for Beta-uniform model |
| rbetauniform | Random draw function for Beta-uniform model |
| show-BetaUniformModel-method | Simple summary printer for a beta-uniform fit |
| siTAZdiffex_HFL1_diffexDT | Differential expression from RNAseq assay of TAZ siRNA... |
| trueNegativeFraction | True negative rate from M&P: D table 1 and equation 5 |
| truePositiveFraction | True positive rate from M&P: A in table 1 and equation 5 |
| TTRUST_TF2targets_DT | A Manually Curated Dataset Of Human Transcription Factor -... |
| uniformComponentBound | Upper bound on Uniform component of Beta-uniform model |
| WZ4002_adrH1975_diffexDT | Microarray assay studying aberrant MAPK1/ERK signaling,... |
