Man pages for steveped/BMEA
Bayesian Modelling for Exon Arrays
| AffymetrixCelSetList | Make a list object where each element is an AffymetrixCelSet |
| assignBgPriors | Assign the Background Signal Priors for each PM probe |
| BMEA-package | Bayesian Modelling for Exon Arrays |
| boxplotPhi | Draws a boxplot of the phi distribution for all exons/groups. |
| clearNodes | Remove all files/folders used on each node |
| createCelHeader | Create a CEL header from the supplied inputs |
| defineGcBins | Estimate the mean and standard deviation for the log... |
| defineMatBins | Define the bins, mean & sd for log background signal using... |
| extractBmeaArray | Extract the data from an AffymetrixCelSetList as an array or... |
| fitBackgroundParameters | Estimate the parameters for the Background Signal. |
| fitBmea | Fit the BMEA model for a large number of units |
| fitBmeaBatch | Fit the BMEA model for a single batch of units |
| fitBmeaSingle | Fit & summarise the BMEA model for a single gene(unit) |
| fitBmea.Snow | Fit the BMEA process for a number of genes utilising the snow... |
| gcCounts | Get the number of GC bases from a batch of sequences. |
| getLogFC | Sample the log fold-change from a BMEA.MCMC dataset |
| getPhiLogFC | Sample the log fold-change for each exon from a BMEA.MCMC... |
| isBMEA | Check the class & structure of BMEA objects |
| mergeNodes | Merge the CEL files written on multiple nodes into a single... |
| runMCMC.BMEA | Fit the BMEA model for a single gene. |
| setMatMatrix | Define the MAT model matrix for an given set of sequences |
| summariseChains | Summarise the output of the BMEA MCMC process |
| unitLine | Add the Unit Line to a plot |
| units2bed | Export a BED file(s) for a given set of units |
| volcanoPlot.BMEA | Draw a volcano plot from a BMEA array |
| writeBmeaBatch | Write the parameters to disk for a batch of genes |
| zScore | Calculate the Z-Score for a given transcript/unit |
