analyzeComparative | Run a comparative analysis between conditions |
analyzeQuantification | Perform quantitative analysis on the MPRA data. This analysis... |
ChrEpi | Sample MPRA data |
estimateDepthFactors | estimate library size correction factors |
extractModelParameters | extract the DNA model parameters |
getAlpha | return the fitted value for the transcription rate. |
getDistrParam | Get model distribution parameters from an MpraObject of a... |
getFits_DNA | Get DNA model-based estimates from an MpraObject (the... |
getFits_RNA | Get RNA model-based estimates from an MpraObject (the... |
MpraObject | MpraObject |
setDepthFactors | Manually set library depth correction factors |
setModel | Set the distributional model used. Default is gamma.pois, and... |
simulateMPRA | Simulate an MPRA dataset |
testCoefficient | Calculate the significance of a factor in the regression... |
testEmpirical | test for significant activity (quantitative analysis) using... |
testLrt | Calculate likelihood ratio test for the specific nested model |
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