Man pages for PriceLab/TrenaProject
TrenaProject - an abstract base class for all projects
| getAllTranscriptionFactors | get all genes annotated by GO to |
| getCovariateDataset | Get the specified covariates table |
| getCovariateDatasetNames | List the RData files in the covariate directory |
| getDataDirectory | Get the names of the expression directory, wherein serialized... |
| getExpressionMatrix | Get the a specifc expression matrix |
| getExpressionMatrixNames | Get the names of the expression matrices - their names with... |
| getFootprintDatabaseHost | get the host on which the footprints Postgres database is... |
| getFootprintDatabaseNames | get the names of the database tables holding footprints |
| getFootprintDatabasePort | get the port on which the footprints Postgres database is... |
| getGeneInfoTable | return the data.frame with gene ids, chromosome, tss of the... |
| getGeneRegion | Get the chromosomal region surrounding the current... |
| getGenome | get the genome name - to be set by derived classes |
| getProjectName | get the project name - to be set by derived classes |
| getProximalPromoter | Get the chromosomal region surrounding the current... |
| getRegionDatasetNames | Get a list of datasets each describing regions of interest,... |
| getSupportedGenes | get the list of genes supported in this project |
| getTargetGene | get the single gene currently designated for analysis |
| getTranscriptsTable | Get the transcript info for the gene, just the first row |
| getVariantDataset | Get the specified variants table |
| getVariantDatasetNames | List the RData files in the variants directory |
| recognizedGene | Do we have expression data for the suggested gene? genomic... |
| setTargetGene | Set a single gene for analysis |
| show | get a summary of the objects |
| TrenaProject-class | TrenaProject |
