demi: Differential Expression from Multiple Indicators

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
http://biit.cs.ut.ee/demi

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.