analyzeComparative | Run a comparative analysis between conditions |
analyzeQuantification | Perform quantitative analysis on the MPRA data. This analysis aims to determine which sequences have a regulatory function, when no condition is being tested. |
ce.colAnnot | Sample MPRA data |
ce.control | Sample MPRA data |
ce.dnaCounts | Sample MPRA data |
ce.rnaCounts | Sample MPRA data |
ChrEpi | Sample MPRA data |
controls | MpraObject |
controls-method | MpraObject |
dnaAnnot | MpraObject |
dnaAnnot-method | MpraObject |
dnaCounts | MpraObject |
dnaCounts-method | MpraObject |
dnaDepth | MpraObject |
dnaDepth-method | MpraObject |
estimateDepthFactors | estimate library size correction factors |
extractModelParameters_DNA | extract the DNA model parameters |
extractModelParameters_RNA | extract the DNA model parameters |
getAlpha | return the fitted value for the transcription rate. |
getDistrParam_DNA | Get model distribution parameters from an MpraObject of a given candidate enhancer |
getDistrParam_RNA | Get model distribution parameters from an MpraObject of a given candidate enhancer |
getFits_DNA | Get DNA model-based estimates from an MpraObject (the expected values based on the model). These can be compared with the observed counts to assess goodness of fit. |
getFits_RNA | Get RNA model-based estimates from an MpraObject (the expected values based on the model). These can be compared with the observed counts to assess goodness of fit. |
getModelParameters_DNA | extract the DNA model parameters |
getModelParameters_RNA | extract the DNA model parameters |
model | MpraObject |
model-method | MpraObject |
MpraObject | MpraObject |
MpraObject-method | MpraObject |
rnaAnnot | MpraObject |
rnaAnnot-method | MpraObject |
rnaCounts | MpraObject |
rnaCounts-method | MpraObject |
rnaDepth | MpraObject |
rnaDepth-method | MpraObject |
rowAnnot | MpraObject |
rowAnnot-method | MpraObject |
setDepthFactors | Manually set library depth correction factors |
setModel | Set the distributional model used. Default is gamma.pois, and is recommended. Other supoprted models are ln.nb in which the DNA follows a log-normal distribution and the RNA follows a negative binomial, and ln.ln in which both follow log-normal distributions. To use alternative distributional models, use this function before fitting the model. |
simulateMPRA | Simulate an MPRA dataset |
testCoefficient | Calculate the significance of a factor in the regression model |
testEmpirical | test for significant activity (quantitative analysis) using various empirical tests (see details) |
testLrt | Calculate likelihood ratio test for the specific nested model |