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