Man pages for demi
Differential Expression from Multiple Indicators
| addCustomTargets-methods | Add new alignments to the alignment table |
| addCytoband-methods | Add karyotype information to DEMI differential expression... |
| adjust4maxprobes-methods | Adjust the DEMI analysis by 'maxprobes' analysis |
| attachResult-methods | Attach results from 'DEMIDiff' object to 'DEMIExperiment'... |
| calcHypergeoExon-methods | Calculates hypergeometric probability in DEMI analysis |
| calcHypergeoProb-methods | Calculates hypergeometric probability in DEMI analysis |
| celMatrixNormalize-methods | Initializes the normalization of the raw expression matrix |
| check4probe-methods | Checks if the probes are available |
| check4target-methods | Checks if the targets are available |
| checkDEMIExperiment_analysis | Checks if the 'analysis' is correct |
| checkDEMIExperiment_celpath | Checks if 'celpath' is correct |
| checkDEMIExperiment_experiment | Checks if the 'experiment' is correct |
| checkDEMIExperiment_maxprobes | Checks if 'maxprobes' is correct |
| checkDEMIExperiment_maxtargets | Checks if 'maxtargets' is correct |
| checkDEMIExperiment_normalization | Checks if 'normormalization' is correct |
| checkDEMIExperiment_pmsize | Checks if 'pmsize' is correct |
| cleanorganismname-methods | Cleans the organism name from redundant characters |
| cluster-methods | Initializes the clustering of probes into clusters |
| createGroup-methods | Creates a 'DEMIGroup' object |
| customObject-methods | Checks if the 'DEMIClust' object is user defined or... |
| DEMICel-class | Class 'DEMICel' |
| DEMICel-methods | Creates a 'DEMICel' object |
| DEMIClust-class | Class 'DEMIClust' |
| DEMIClust-methods | Creates a 'DEMIClust' object |
| demi.comp.test-methods | Cluster probes into higher and lower clusters based on their... |
| DEMIDiff-class | Class 'DEMIDiff' |
| DEMIDiff-methods | Creates a 'DEMIDiff' object |
| demiequal-methods | Cluster probes that have no statistically significant... |
| DEMIExperiment-class | Class 'DEMIExperiment' |
| DEMIExperiment-methods | Creates a 'DEMIExperiment' object |
| DEMIGroup-class | Class 'DEMIGroup' |
| DEMIGroup-methods | Creates a 'DEMIGroup' object |
| DEMIMessages | A 'list' of DEMI messages |
| DEMIPathway-methods | Functional annotation of DEMI results |
| DEMIResult-class | Class 'DEMIResult' |
| demisummary-methods | Returns the mean normalized expression levels for the... |
| demi.t.test-methods | Cluster probes into higher and lower clusters based on their... |
| demi.wilcox.test.fast-methods | Cluster probes into higher and lower clusters based on their... |
| demi.wilcox.test-methods | Cluster probes into higher and lower clusters based on their... |
| DEMIWrap-methods | A wrapper for DEMI analysis |
| diffexp-methods | Initializes the differential expression analysis |
| diffSpliceScore-methods | Calculate differential splice scores |
| findCytoband-methods | Finds cytoband for the specified genome region |
| getAlignment-methods | Returns the 'blatTable' parameter representing alignment... |
| getAnalysis-methods | Returns the 'analysis' parameter |
| getAnnotation-methods | Returns the 'annoTable' parameter representing annotation... |
| getArraytype-methods | Returns the 'arraytype' parameter |
| getCelMatrix-methods | Returns the raw expression matrix |
| getCelpath-methods | Returns the 'celpath' parameter |
| getCluster-methods | Returns the 'cluster' parameter |
| getClustMethod-methods | Returns the 'clust.method' parameter |
| getCutoffPvalue-methods | Returns the 'cutoff.pvalue' parameter |
| getCytoband-methods | Returns the 'cytoband' parameter representing karyotype... |
| getDEMIClust-methods | Returns the 'cluster' parameter |
| getExperiment-methods | Returns the 'experiment' parameter |
| getGroupA-methods | Returns the 'groupA' parameter |
| getGroupB-methods | Returns the 'groupB' parameter |
| getGroup-methods | Returns the 'group' parameter |
| getGroupNames-methods | Returns the 'groupNames' parameter |
| getIndexA-methods | Returns the 'indexA' parameter |
| getIndexB-methods | Returns the 'indexB' parameter |
| getMaxprobes-methods | Returns the 'maxprobes' parameter |
| getMaxtargets-methods | Returns the 'maxtargets' parameter |
| getName-methods | Returns the 'name' parameter |
| getNormMatrix-methods | Returns the normalized expression matrix |
| getOrganism-methods | Returns the 'organism' parameter |
| getPathway-methods | Returns the 'pathway' parameter representing functional... |
| getProbeLevel-methods | Returns the probe levels from the normalized expression... |
| getResult-methods | Returns the 'result' parameter |
| getResultTable-methods | Retruns the DEMI analysis results as a 'data.frame' |
| getTargetAnnotation-methods | Returns annotation information for the specified targets |
| getTargetProbes-methods | Returns the probe ID's of the specified targets |
| initialize.DEMICel | Initializes a 'DEMICel' object |
| initialize.DEMIClust | Initializes the 'DEMIClust' object |
| initialize.DEMIDiff | Initializes the 'DEMIDiff' object |
| initialize.DEMIExperiment | Initializes the 'DEMIExperiment' object |
| initialize.DEMIGroup | Initializes the 'DEMIGroup' object |
| initialize.DEMIResult | Initializes the 'DEMIResult' object |
| loadAnnotation-methods | Loads the annotation information specified by the... |
| loadBlat-methods | Loads the alignment information specified by the... |
| loadCel-methods | Loads the raw expression matrix into a 'DEMIExperiment'... |
| loadCytoband-methods | Loads the karyotype information specified by the... |
| loadDEMILibrary-methods | Loads the DEMI annotation package specified by the... |
| loadPathway-methods | Loads the pathway information specified by the... |
| makeDEMIResultsTable-methods | Returns a 'data.frame' of the differential expression results |
| makeUCSCLink-methods | Make UCSC link |
| matchExonGene-methods | Matches exons to their corresponding transcripts. |
| norm.quantile-methods | Quantile normalization function |
| norm.rrank-methods | Relative rank normalization function |
| probe.levels-methods | Draws a histogram of the normalized expression levels of the... |
| probe.plot-methods | Draws a plot of the normalized expression levels of the... |
| totalMatches_all-methods | Calculates the number of matches over all probes |
| totalMatches_cluster-methods | Calculates the number of matches in the cluster |
| validDEMIClust | Validates the 'DEMIClust' object |
| validDEMIExperiment | Validates the 'DEMIExperiment' object |
| wprob-methods | Calculates wilcoxon's upper and lower probabilities |
