Statistical Analysis of MPRA data

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Documentation for package ‘MPRAnalyze’ version 1.18.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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