Differential Expression from Multiple Indicators


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Documentation for package ‘demi’ version 1.1.2

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A C D F G I L M N P T V W

-- A --

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

-- C --

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

-- D --

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

-- F --

findCytoband Finds cytoband for the specified genome region

-- G --

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

-- I --

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

-- L --

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

-- M --

makeDEMIResultsTable Returns a 'data.frame' of the differential expression results
makeUCSCLink Make UCSC link
matchExonGene Matches exons to their corresponding transcripts.

-- N --

norm.quantile Quantile normalization function
norm.quantile-method Quantile normalization function
norm.rrank Relative rank normalization function
norm.rrank-method Relative rank normalization function

-- P --

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

-- T --

totalMatches_all Calculates the number of matches over all probes
totalMatches_cluster Calculates the number of matches in the cluster

-- V --

validDEMIClust Validates the 'DEMIClust' object
validDEMIExperiment Validates the 'DEMIExperiment' object

-- W --

wprob Calculates wilcoxon's upper and lower probabilities