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 |