Man pages for MBASED
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
| betaParametrizationConverters | Functions to convert between shape parameters a and b for... |
| estimateMAF1s | Function that given observed count data returns a maximum... |
| estimateMAF2s | Function that given observed count data returns a maximum... |
| FreemanTukeyFunctions | Freeman-Tukey transformation functions. |
| generatingBetaBinomialCounts | Functions to generate beta-binomial random variables. |
| getPFinal | Function that adjusts true underlying allele frequency for... |
| getSimulationPvalue | Function to calculate simulations-based p-values |
| logLikelihoodCalculator1s | Function that given observed count data along a known... |
| logLikelihoodCalculator2s | Function that given observed count data along a known... |
| maxLogLikelihoodCalculator1s | Function that given observed count data along a known... |
| maxLogLikelihoodCalculator2s | Function that given observed count data along a known... |
| MBASED | MBASED |
| MBASEDMetaAnalysis | Generic function to perform standard meta analysis. |
| MBASEDMetaAnalysisGetMeansAndSEs | Helper function to obtain estimate of underlying mean and the... |
| MBASEDVectorizedMetaprop | Vectorized wrapper around metaprop() function from R package... |
| MBASEDVectorizedPropDiffTest | Vectorized wrapper around a test for difference of 2... |
| runMBASED | Main function that implements MBASED. |
| runMBASED1s | Function that runs single-sample ASE calling using data from... |
| runMBASED1s1aseID | Function that runs single-sample ASE calling using data from... |
| runMBASED2s | Function that runs between-sample (differential) ASE calling... |
| runMBASED2s1aseID | Function that runs between-sample (differential) ASE calling... |
| shiftAndAttenuateProportions | Helper function to adjust proportions for pre-existing... |
| testNumericDiff | Function that checks to see if the difference between 2... |
| testQuantiles | Function to test quantile equality for theoretical and... |
