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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MBASED")
AuthorOleg Mayba, Houston Gilbert
Bioconductor views GeneExpression Sequencing Transcription
Date of publicationNone
MaintainerOleg Mayba <mayba.oleg@gene.com>
LicenseArtistic-2.0
Version1.10.0

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...

Functions

estimateMAF1s Man page
estimateMAF2s Man page
FT Man page
FTAdjust Man page
getAB Man page
getMuRho Man page
getPFinal Man page
getSimulationPvalue Man page
isCountMajorFT Man page
logLikelihoodCalculator1s Man page
logLikelihoodCalculator2s Man page
maxLogLikelihoodCalculator1s Man page
maxLogLikelihoodCalculator2s Man page
MBASED Man page
MBASEDMetaAnalysis Man page
MBASEDMetaAnalysisGetMeansAndSEs Man page
MBASED-package Man page
MBASEDVectorizedMetaprop Man page
MBASEDVectorizedPropDiffTest Man page
runMBASED Man page
runMBASED1s Man page
runMBASED1s1aseID Man page
runMBASED2s Man page
runMBASED2s1aseID Man page
shiftAndAttenuateProportions Man page
testNumericDiff Man page
testQuantiles Man page
unFT Man page
vectorizedRbetabinomAB Man page
vectorizedRbetabinomMR Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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