R: Statistical Analysis of MPRA data

# Statistical Analysis of MPRA data

## Documentation for package ‘MPRAnalyze’ version 1.31.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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