Man pages for steveped/BMEA
Bayesian Modelling for Exon Arrays

AffymetrixCelSetListMake a list object where each element is an AffymetrixCelSet
assignBgPriorsAssign the Background Signal Priors for each PM probe
BMEA-packageBayesian Modelling for Exon Arrays
boxplotPhiDraws a boxplot of the phi distribution for all exons/groups.
clearNodesRemove all files/folders used on each node
createCelHeaderCreate a CEL header from the supplied inputs
defineGcBinsEstimate the mean and standard deviation for the log...
defineMatBinsDefine the bins, mean & sd for log background signal using...
extractBmeaArrayExtract the data from an AffymetrixCelSetList as an array or...
fitBackgroundParametersEstimate the parameters for the Background Signal.
fitBmeaFit the BMEA model for a large number of units
fitBmeaBatchFit the BMEA model for a single batch of units
fitBmeaSingleFit & summarise the BMEA model for a single gene(unit)
fitBmea.SnowFit the BMEA process for a number of genes utilising the snow...
gcCountsGet the number of GC bases from a batch of sequences.
getLogFCSample the log fold-change from a BMEA.MCMC dataset
getPhiLogFCSample the log fold-change for each exon from a BMEA.MCMC...
isBMEACheck the class & structure of BMEA objects
mergeNodesMerge the CEL files written on multiple nodes into a single...
runMCMC.BMEAFit the BMEA model for a single gene.
setMatMatrixDefine the MAT model matrix for an given set of sequences
summariseChainsSummarise the output of the BMEA MCMC process
unitLineAdd the Unit Line to a plot
units2bedExport a BED file(s) for a given set of units
volcanoPlot.BMEADraw a volcano plot from a BMEA array
writeBmeaBatchWrite the parameters to disk for a batch of genes
zScoreCalculate the Z-Score for a given transcript/unit
steveped/BMEA documentation built on Oct. 23, 2018, 4:20 p.m.