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.

AuthorOleg Mayba, Houston Gilbert
Date of publicationNone
MaintainerOleg Mayba <mayba.oleg@gene.com>
LicenseArtistic-2.0
Version1.8.0

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

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