Statistical Analysis of MPRA data


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Documentation for package ‘MPRAnalyze’ version 1.18.0

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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