demi: Differential Expression from Multiple Indicators
Version 1.1.2

Implementation of the DEMI method for the analysis of high-density microarray data.

AuthorSten Ilmjarv [aut, cre], Hendrik Luuk [aut]
Date of publication2015-02-13 20:22:57
MaintainerSten Ilmjarv <sten.ilmjarv@gmail.com>
LicenseGPL (>= 2)
Version1.1.2
URL http://biit.cs.ut.ee/demi
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("demi")

Popular man pages

calcHypergeoExon-methods: Calculates hypergeometric probability in DEMI analysis
customObject-methods: Checks if the 'DEMIClust' object is user defined or...
DEMIClust-methods: Creates a 'DEMIClust' object
getAlignment-methods: Returns the 'blatTable' parameter representing alignment...
getAnalysis-methods: Returns the 'analysis' parameter
getMaxprobes-methods: Returns the 'maxprobes' parameter
loadCel-methods: Loads the raw expression matrix into a 'DEMIExperiment'...
See all...

All man pages Function index File listing

Man pages

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

Functions

DEMICel Man page
DEMICel-class Man page
DEMIClust Man page
DEMIClust-class Man page
DEMIDiff Man page
DEMIDiff-class Man page
DEMIExperiment Man page
DEMIExperiment-class Man page
DEMIGroup Man page
DEMIGroup-class Man page
DEMIMessages Man page
DEMIPathway Man page
DEMIResult-class Man page
addCustomTargets Man page
addCytoband Man page
adjust4maxprobes Man page Source code
attachResult Man page
attachResult,DEMIExperiment,DEMIDiff-method Man page
calcHypergeoExon Man page Source code
calcHypergeoProb Man page Source code
celMatrixNormalize Man page
celMatrixNormalize,DEMIExperiment,function-method Man page
check4probe Man page
check4probe,DEMIExperiment,vector-method Man page
check4target Man page
check4target,DEMIExperiment,vector-method Man page
checkDEMIExperiment_analysis Man page Source code
checkDEMIExperiment_celpath Man page Source code
checkDEMIExperiment_experiment Man page Source code
checkDEMIExperiment_maxprobes Man page Source code
checkDEMIExperiment_maxtargets Man page Source code
checkDEMIExperiment_normalization Man page Source code
checkDEMIExperiment_pmsize Man page Source code
cleanorganismname Man page Source code
cluster Man page
cluster,DEMIClust-method Man page
createGroup Man page
createGroup,DEMIClust-method Man page
customObject Man page
customObject,DEMIClust-method Man page
demi Man page
demi.comp.test Man page
demi.t.test Man page
demi.wilcox.test Man page
demi.wilcox.test.fast Man page
demiequal Man page
demisummary Man page
demisummary,DEMIDiff-method Man page
demisummary,DEMIExperiment-method Man page
diffSpliceScore Man page Source code
diffexp Man page
diffexp,DEMIDiff-method Man page
findCytoband Man page
getAlignment Man page
getAlignment,DEMIExperiment-method Man page
getAnalysis Man page
getAnalysis,DEMIExperiment-method Man page
getAnnotation Man page
getAnnotation,DEMIExperiment-method Man page
getArraytype Man page
getArraytype,DEMIExperiment-method Man page
getCelMatrix Man page
getCelMatrix,DEMIExperiment-method Man page
getCelpath Man page
getCelpath,DEMIExperiment-method Man page
getClustMethod Man page
getClustMethod,DEMIClust-method Man page
getCluster Man page
getCluster,DEMIClust-method Man page
getCutoffPvalue Man page
getCutoffPvalue,DEMIClust-method Man page
getCytoband Man page
getCytoband,DEMIExperiment-method Man page
getDEMIClust Man page
getDEMIClust,DEMIDiff-method Man page
getExperiment Man page
getExperiment,DEMIClust-method Man page
getExperiment,DEMIDiff-method Man page
getExperiment,DEMIExperiment-method Man page
getGroup Man page
getGroup,DEMIClust-method Man page
getGroup,DEMIDiff-method Man page
getGroup,DEMIResult-method Man page
getGroupA Man page
getGroupA,DEMIGroup-method Man page
getGroupB Man page
getGroupB,DEMIGroup-method Man page
getGroupNames Man page
getGroupNames,DEMIGroup-method Man page
getIndexA Man page
getIndexA,DEMIGroup-method Man page
getIndexB Man page
getIndexB,DEMIGroup-method Man page
getMaxprobes Man page
getMaxprobes,DEMIExperiment-method Man page
getMaxtargets Man page
getMaxtargets,DEMIExperiment-method Man page
getName Man page
getName,DEMIDiff-method Man page
getNormMatrix Man page
getNormMatrix,DEMIExperiment-method Man page
getOrganism Man page
getOrganism,DEMIExperiment-method Man page
getPathway Man page
getPathway,DEMIExperiment-method Man page
getProbeLevel Man page
getProbeLevel,DEMIDiff,vector,logical-method Man page
getProbeLevel,DEMIExperiment,vector,logical-method Man page
getResult Man page
getResult,DEMIDiff-method Man page
getResult,DEMIExperiment-method Man page
getResult,DEMIResult-method Man page
getResultTable Man page
getResultTable,DEMIDiff-method Man page
getResultTable,DEMIExperiment-method Man page
getTargetAnnotation Man page
getTargetAnnotation,DEMIExperiment,vector-method Man page
getTargetProbes Man page
getTargetProbes,DEMIDiff,vector-method Man page
getTargetProbes,DEMIExperiment,vector-method Man page
initialize.DEMICel Man page
initialize.DEMIClust Man page
initialize.DEMIDiff Man page
initialize.DEMIExperiment Man page
initialize.DEMIGroup Man page
initialize.DEMIResult Man page
loadAnnotation Man page
loadAnnotation,DEMIExperiment,environment-method Man page
loadBlat Man page
loadBlat,DEMIExperiment,environment-method Man page
loadCel Man page
loadCel,DEMIExperiment-method Man page
loadCytoband Man page
loadCytoband,DEMIExperiment,environment-method Man page
loadDEMILibrary Man page
loadDEMILibrary,DEMIExperiment-method Man page
loadPathway Man page
loadPathway,DEMIExperiment,environment-method Man page
makeDEMIResultsTable Man page
makeUCSCLink Man page
matchExonGene Man page Source code
norm.quantile Man page
norm.quantile,matrix-method Man page
norm.rrank Man page
norm.rrank,matrix-method Man page
norm.rrank,numeric-method Man page
onAttach Source code
probe.levels Man page
probe.levels,DEMIExperiment,character-method Man page
probe.plot Man page
probe.plot,DEMIExperiment,character-method Man page
totalMatches_all Man page Source code
totalMatches_cluster Man page Source code
validDEMIClust Man page
validDEMIExperiment Man page
wprob Man page

Files

inst
inst/doc
inst/doc/demi.pdf
inst/doc/demi.Rnw
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/cytoband-methods.R
R/normalization-methods.R
R/DEMIResult-methods.R
R/cluster-methods.R
R/DEMIExperiment-methods.R
R/messages.R
R/DEMIGroup-methods.R
R/DEMIDiff-methods.R
R/DEMICel-methods.R
R/Constructors.R
R/custom-methods.R
R/diffexp-methods.R
R/DEMIClust-methods.R
R/zzz.R
R/other-methods.R
vignettes
vignettes/MAOB_probe_levels.pdf
vignettes/demi.Rnw
vignettes/references.bib
vignettes/MAOB_probe_plot.pdf
MD5
build
build/vignette.rds
DESCRIPTION
man
man/calcHypergeoExon-methods.Rd
man/getPathway-methods.Rd
man/findCytoband-methods.Rd
man/getDEMIClust-methods.Rd
man/DEMIGroup-class.Rd
man/getResult-methods.Rd
man/loadDEMILibrary-methods.Rd
man/getGroup-methods.Rd
man/initialize.DEMIGroup.Rd
man/getCelpath-methods.Rd
man/makeDEMIResultsTable-methods.Rd
man/checkDEMIExperiment_celpath.Rd
man/demi.wilcox.test.fast-methods.Rd
man/check4probe-methods.Rd
man/getOrganism-methods.Rd
man/norm.rrank-methods.Rd
man/DEMICel-methods.Rd
man/getProbeLevel-methods.Rd
man/probe.plot-methods.Rd
man/loadAnnotation-methods.Rd
man/getMaxtargets-methods.Rd
man/loadCel-methods.Rd
man/DEMIExperiment-class.Rd
man/checkDEMIExperiment_maxprobes.Rd
man/DEMIDiff-methods.Rd
man/getMaxprobes-methods.Rd
man/getCutoffPvalue-methods.Rd
man/makeUCSCLink-methods.Rd
man/demi.t.test-methods.Rd
man/checkDEMIExperiment_maxtargets.Rd
man/attachResult-methods.Rd
man/DEMIResult-class.Rd
man/initialize.DEMICel.Rd
man/DEMICel-class.Rd
man/cleanorganismname-methods.Rd
man/DEMIGroup-methods.Rd
man/getGroupA-methods.Rd
man/getNormMatrix-methods.Rd
man/getExperiment-methods.Rd
man/customObject-methods.Rd
man/diffSpliceScore-methods.Rd
man/getCluster-methods.Rd
man/totalMatches_all-methods.Rd
man/createGroup-methods.Rd
man/DEMIDiff-class.Rd
man/demi.comp.test-methods.Rd
man/matchExonGene-methods.Rd
man/checkDEMIExperiment_analysis.Rd
man/wprob-methods.Rd
man/initialize.DEMIClust.Rd
man/initialize.DEMIResult.Rd
man/getAlignment-methods.Rd
man/validDEMIClust.Rd
man/celMatrixNormalize-methods.Rd
man/DEMIExperiment-methods.Rd
man/DEMIPathway-methods.Rd
man/getGroupB-methods.Rd
man/demiequal-methods.Rd
man/getName-methods.Rd
man/getClustMethod-methods.Rd
man/loadPathway-methods.Rd
man/initialize.DEMIDiff.Rd
man/diffexp-methods.Rd
man/loadBlat-methods.Rd
man/getResultTable-methods.Rd
man/cluster-methods.Rd
man/DEMIWrap-methods.Rd
man/getAnalysis-methods.Rd
man/checkDEMIExperiment_normalization.Rd
man/DEMIClust-methods.Rd
man/initialize.DEMIExperiment.Rd
man/getGroupNames-methods.Rd
man/loadCytoband-methods.Rd
man/getIndexB-methods.Rd
man/totalMatches_cluster-methods.Rd
man/calcHypergeoProb-methods.Rd
man/adjust4maxprobes-methods.Rd
man/getAnnotation-methods.Rd
man/getCelMatrix-methods.Rd
man/addCustomTargets-methods.Rd
man/demi.wilcox.test-methods.Rd
man/probe.levels-methods.Rd
man/getIndexA-methods.Rd
man/checkDEMIExperiment_pmsize.Rd
man/norm.quantile-methods.Rd
man/checkDEMIExperiment_experiment.Rd
man/getTargetAnnotation-methods.Rd
man/check4target-methods.Rd
man/validDEMIExperiment.Rd
man/DEMIClust-class.Rd
man/getArraytype-methods.Rd
man/DEMIMessages.Rd
man/addCytoband-methods.Rd
man/getCytoband-methods.Rd
man/getTargetProbes-methods.Rd
man/demisummary-methods.Rd
demi documentation built on May 20, 2017, 12:42 a.m.

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