demi: Differential Expression from Multiple Indicators

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

Author
Sten Ilmjarv [aut, cre], Hendrik Luuk [aut]
Date of publication
2015-02-13 20:22:57
Maintainer
Sten Ilmjarv <sten.ilmjarv@gmail.com>
License
GPL (>= 2)
Version
1.1.2
URLs

View on CRAN

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

Files in this package

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