MBASED: Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection

The package implements MBASED algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE.

Author
Oleg Mayba, Houston Gilbert
Date of publication
None
Maintainer
Oleg Mayba <mayba.oleg@gene.com>
License
Artistic-2.0
Version
1.8.0

View on Bioconductor

Man pages

betaParametrizationConverters
Functions to convert between shape parameters a and b for...
estimateMAF1s
Function that given observed count data returns a maximum...
estimateMAF2s
Function that given observed count data returns a maximum...
FreemanTukeyFunctions
Freeman-Tukey transformation functions.
generatingBetaBinomialCounts
Functions to generate beta-binomial random variables.
getPFinal
Function that adjusts true underlying allele frequency for...
getSimulationPvalue
Function to calculate simulations-based p-values
logLikelihoodCalculator1s
Function that given observed count data along a known...
logLikelihoodCalculator2s
Function that given observed count data along a known...
maxLogLikelihoodCalculator1s
Function that given observed count data along a known...
maxLogLikelihoodCalculator2s
Function that given observed count data along a known...
MBASED
MBASED
MBASEDMetaAnalysis
Generic function to perform standard meta analysis.
MBASEDMetaAnalysisGetMeansAndSEs
Helper function to obtain estimate of underlying mean and the...
MBASEDVectorizedMetaprop
Vectorized wrapper around metaprop() function from R package...
MBASEDVectorizedPropDiffTest
Vectorized wrapper around a test for difference of 2...
runMBASED
Main function that implements MBASED.
runMBASED1s
Function that runs single-sample ASE calling using data from...
runMBASED1s1aseID
Function that runs single-sample ASE calling using data from...
runMBASED2s
Function that runs between-sample (differential) ASE calling...
runMBASED2s1aseID
Function that runs between-sample (differential) ASE calling...
shiftAndAttenuateProportions
Helper function to adjust proportions for pre-existing...
testNumericDiff
Function that checks to see if the difference between 2...
testQuantiles
Function to test quantile equality for theoretical and...

Files in this package

MBASED/DESCRIPTION
MBASED/NAMESPACE
MBASED/R
MBASED/R/MBASEDBetaBinomialFunctions.R
MBASED/R/MBASEDPackageStatement.R
MBASED/R/MBASEDStatsHelperFunctions1s.R
MBASED/R/MBASEDStatsHelperFunctions2s.R
MBASED/R/MBASEDStatsMainFunctions1s.R
MBASED/R/MBASEDStatsMainFunctions2s.R
MBASED/R/MBASEDStatsMainFunctionsExport.R
MBASED/R/MBASEDUnitTestsFunctions.R
MBASED/build
MBASED/build/vignette.rds
MBASED/inst
MBASED/inst/NEWS
MBASED/inst/doc
MBASED/inst/doc/MBASED.R
MBASED/inst/doc/MBASED.Rnw
MBASED/inst/doc/MBASED.pdf
MBASED/inst/unitTests
MBASED/inst/unitTests/test_FT_functions.R
MBASED/inst/unitTests/test_MBASED_1s_method.R
MBASED/inst/unitTests/test_MBASED_2s_method.R
MBASED/inst/unitTests/test_betabinomial_functions.R
MBASED/inst/unitTests/test_miscellaneous_helper_functions.R
MBASED/man
MBASED/man/FreemanTukeyFunctions.Rd
MBASED/man/MBASED.Rd
MBASED/man/MBASEDMetaAnalysis.Rd
MBASED/man/MBASEDMetaAnalysisGetMeansAndSEs.Rd
MBASED/man/MBASEDVectorizedMetaprop.Rd
MBASED/man/MBASEDVectorizedPropDiffTest.Rd
MBASED/man/betaParametrizationConverters.Rd
MBASED/man/estimateMAF1s.Rd
MBASED/man/estimateMAF2s.Rd
MBASED/man/generatingBetaBinomialCounts.Rd
MBASED/man/getPFinal.Rd
MBASED/man/getSimulationPvalue.Rd
MBASED/man/logLikelihoodCalculator1s.Rd
MBASED/man/logLikelihoodCalculator2s.Rd
MBASED/man/maxLogLikelihoodCalculator1s.Rd
MBASED/man/maxLogLikelihoodCalculator2s.Rd
MBASED/man/runMBASED.Rd
MBASED/man/runMBASED1s.Rd
MBASED/man/runMBASED1s1aseID.Rd
MBASED/man/runMBASED2s.Rd
MBASED/man/runMBASED2s1aseID.Rd
MBASED/man/shiftAndAttenuateProportions.Rd
MBASED/man/testNumericDiff.Rd
MBASED/man/testQuantiles.Rd
MBASED/tests
MBASED/tests/runTests.R
MBASED/vignettes
MBASED/vignettes/MBASED.Rnw