Man pages for demi
Differential Expression from Multiple Indicators

addCustomTargets-methodsAdd new alignments to the alignment table
addCytoband-methodsAdd karyotype information to DEMI differential expression...
adjust4maxprobes-methodsAdjust the DEMI analysis by 'maxprobes' analysis
attachResult-methodsAttach results from 'DEMIDiff' object to 'DEMIExperiment'...
calcHypergeoExon-methodsCalculates hypergeometric probability in DEMI analysis
calcHypergeoProb-methodsCalculates hypergeometric probability in DEMI analysis
celMatrixNormalize-methodsInitializes the normalization of the raw expression matrix
check4probe-methodsChecks if the probes are available
check4target-methodsChecks if the targets are available
checkDEMIExperiment_analysisChecks if the 'analysis' is correct
checkDEMIExperiment_celpathChecks if 'celpath' is correct
checkDEMIExperiment_experimentChecks if the 'experiment' is correct
checkDEMIExperiment_maxprobesChecks if 'maxprobes' is correct
checkDEMIExperiment_maxtargetsChecks if 'maxtargets' is correct
checkDEMIExperiment_normalizationChecks if 'normormalization' is correct
checkDEMIExperiment_pmsizeChecks if 'pmsize' is correct
cleanorganismname-methodsCleans the organism name from redundant characters
cluster-methodsInitializes the clustering of probes into clusters
createGroup-methodsCreates a 'DEMIGroup' object
customObject-methodsChecks if the 'DEMIClust' object is user defined or...
DEMICel-classClass 'DEMICel'
DEMICel-methodsCreates a 'DEMICel' object
DEMIClust-classClass 'DEMIClust'
DEMIClust-methodsCreates a 'DEMIClust' object
demi.comp.test-methodsCluster probes into higher and lower clusters based on their...
DEMIDiff-classClass 'DEMIDiff'
DEMIDiff-methodsCreates a 'DEMIDiff' object
demiequal-methodsCluster probes that have no statistically significant...
DEMIExperiment-classClass 'DEMIExperiment'
DEMIExperiment-methodsCreates a 'DEMIExperiment' object
DEMIGroup-classClass 'DEMIGroup'
DEMIGroup-methodsCreates a 'DEMIGroup' object
DEMIMessagesA 'list' of DEMI messages
DEMIPathway-methodsFunctional annotation of DEMI results
DEMIResult-classClass 'DEMIResult'
demisummary-methodsReturns the mean normalized expression levels for the...
demi.t.test-methodsCluster probes into higher and lower clusters based on their...
demi.wilcox.test.fast-methodsCluster probes into higher and lower clusters based on their...
demi.wilcox.test-methodsCluster probes into higher and lower clusters based on their...
DEMIWrap-methodsA wrapper for DEMI analysis
diffexp-methodsInitializes the differential expression analysis
diffSpliceScore-methodsCalculate differential splice scores
findCytoband-methodsFinds cytoband for the specified genome region
getAlignment-methodsReturns the 'blatTable' parameter representing alignment...
getAnalysis-methodsReturns the 'analysis' parameter
getAnnotation-methodsReturns the 'annoTable' parameter representing annotation...
getArraytype-methodsReturns the 'arraytype' parameter
getCelMatrix-methodsReturns the raw expression matrix
getCelpath-methodsReturns the 'celpath' parameter
getCluster-methodsReturns the 'cluster' parameter
getClustMethod-methodsReturns the 'clust.method' parameter
getCutoffPvalue-methodsReturns the 'cutoff.pvalue' parameter
getCytoband-methodsReturns the 'cytoband' parameter representing karyotype...
getDEMIClust-methodsReturns the 'cluster' parameter
getExperiment-methodsReturns the 'experiment' parameter
getGroupA-methodsReturns the 'groupA' parameter
getGroupB-methodsReturns the 'groupB' parameter
getGroup-methodsReturns the 'group' parameter
getGroupNames-methodsReturns the 'groupNames' parameter
getIndexA-methodsReturns the 'indexA' parameter
getIndexB-methodsReturns the 'indexB' parameter
getMaxprobes-methodsReturns the 'maxprobes' parameter
getMaxtargets-methodsReturns the 'maxtargets' parameter
getName-methodsReturns the 'name' parameter
getNormMatrix-methodsReturns the normalized expression matrix
getOrganism-methodsReturns the 'organism' parameter
getPathway-methodsReturns the 'pathway' parameter representing functional...
getProbeLevel-methodsReturns the probe levels from the normalized expression...
getResult-methodsReturns the 'result' parameter
getResultTable-methodsRetruns the DEMI analysis results as a 'data.frame'
getTargetAnnotation-methodsReturns annotation information for the specified targets
getTargetProbes-methodsReturns the probe ID's of the specified targets
initialize.DEMICelInitializes a 'DEMICel' object
initialize.DEMIClustInitializes the 'DEMIClust' object
initialize.DEMIDiffInitializes the 'DEMIDiff' object
initialize.DEMIExperimentInitializes the 'DEMIExperiment' object
initialize.DEMIGroupInitializes the 'DEMIGroup' object
initialize.DEMIResultInitializes the 'DEMIResult' object
loadAnnotation-methodsLoads the annotation information specified by the...
loadBlat-methodsLoads the alignment information specified by the...
loadCel-methodsLoads the raw expression matrix into a 'DEMIExperiment'...
loadCytoband-methodsLoads the karyotype information specified by the...
loadDEMILibrary-methodsLoads the DEMI annotation package specified by the...
loadPathway-methodsLoads the pathway information specified by the...
makeDEMIResultsTable-methodsReturns a 'data.frame' of the differential expression results
makeUCSCLink-methodsMake UCSC link
matchExonGene-methodsMatches exons to their corresponding transcripts.
norm.quantile-methodsQuantile normalization function
norm.rrank-methodsRelative rank normalization function
probe.levels-methodsDraws a histogram of the normalized expression levels of the...
probe.plot-methodsDraws a plot of the normalized expression levels of the...
totalMatches_all-methodsCalculates the number of matches over all probes
totalMatches_cluster-methodsCalculates the number of matches in the cluster
validDEMIClustValidates the 'DEMIClust' object
validDEMIExperimentValidates the 'DEMIExperiment' object
wprob-methodsCalculates wilcoxon's upper and lower probabilities
demi documentation built on May 30, 2017, 2:40 a.m.