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demi (version 1.1.2)

Differential Expression from Multiple Indicators

Description

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

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Version

Install

install.packages('demi')

Monthly Downloads

16

Version

1.1.2

License

GPL (>= 2)

Maintainer

Sten Ilmjarv Developer

Last Published

February 13th, 2015

Functions in demi (1.1.2)

DEMICel

Creates a DEMICel object
checkDEMIExperiment_celpath

Checks if celpath is correct
DEMICel-class

Class DEMICel
calcHypergeoExon

Calculates hypergeometric probability in DEMI analysis
DEMIGroup-class

Class DEMIGroup
DEMIExperiment-class

Class DEMIExperiment
initialize.DEMIExperiment

Initializes the DEMIExperiment object
cleanorganismname

Cleans the organism name from redundant characters
cluster

Initializes the clustering of probes into clusters
checkDEMIExperiment_maxprobes

Checks if maxprobes is correct
getCelMatrix

Returns the raw expression matrix
getOrganism

Returns the organism parameter
initialize.DEMICel

Initializes a DEMICel object
loadAnnotation

Loads the annotation information specified by the DEMIExperiment object
DEMIClust-class

Class DEMIClust
probe.plot

Draws a plot of the normalized expression levels of the specified targets
norm.rrank

Relative rank normalization function
createGroup

Creates a DEMIGroup object
customObject

Checks if the DEMIClust object is user defined or automatically generated
getGroupA

Returns the groupA parameter
makeUCSCLink

Make UCSC link
initialize.DEMIClust

Initializes the DEMIClust object
getNormMatrix

Returns the normalized expression matrix
DEMIClust

Creates a DEMIClust object
getGroup

Returns the group parameter
demi.wilcox.test

Cluster probes into higher and lower clusters based on their differential signalling
diffexp

Initializes the differential expression analysis
DEMIDiff-class

Class DEMIDiff
makeDEMIResultsTable

Returns a data.frame of the differential expression results
totalMatches_cluster

Calculates the number of matches in the cluster
adjust4maxprobes

Adjust the DEMI analysis by maxprobes analysis
checkDEMIExperiment_experiment

Checks if the experiment is correct
demi.t.test

Cluster probes into higher and lower clusters based on their differential signalling
calcHypergeoProb

Calculates hypergeometric probability in DEMI analysis
getIndexA

Returns the indexA parameter
demi

A wrapper for DEMI analysis
findCytoband

Finds cytoband for the specified genome region
check4target

Checks if the targets are available
getTargetAnnotation

Returns annotation information for the specified targets
checkDEMIExperiment_analysis

Checks if the analysis is correct
celMatrixNormalize

Initializes the normalization of the raw expression matrix
getCytoband

Returns the cytoband parameter representing karyotype information
DEMIExperiment

Creates a DEMIExperiment object
getCluster

Returns the cluster parameter
getMaxtargets

Returns the maxtargets parameter
loadDEMILibrary

Loads the DEMI annotation package specified by the DEMIExperiment object
wprob

Calculates wilcoxon's upper and lower probabilities
totalMatches_all

Calculates the number of matches over all probes
DEMIPathway

Functional annotation of DEMI results
DEMIMessages

A list of DEMI messages
DEMIGroup

Creates a DEMIGroup object
addCytoband

Add karyotype information to DEMI differential expression results
demi.comp.test

Cluster probes into higher and lower clusters based on their differential signalling
checkDEMIExperiment_maxtargets

Checks if maxtargets is correct
getGroupNames

Returns the groupNames parameter
probe.levels

Draws a histogram of the normalized expression levels of the specified targets
getAlignment

Returns the blatTable parameter representing alignment information
getArraytype

Returns the arraytype parameter
getProbeLevel

Returns the probe levels from the normalized expression matrix for the specified probes
getAnalysis

Returns the analysis parameter
getClustMethod

Returns the clust.method parameter
loadCel

Loads the raw expression matrix into a DEMIExperiment object
getCutoffPvalue

Returns the cutoff.pvalue parameter
matchExonGene

Matches exons to their corresponding transcripts.
initialize.DEMIResult

Initializes the DEMIResult object
validDEMIClust

Validates the DEMIClust object
initialize.DEMIGroup

Initializes the DEMIGroup object
loadPathway

Loads the pathway information specified by the DEMIExperiment object
loadBlat

Loads the alignment information specified by the DEMIExperiment object
validDEMIExperiment

Validates the DEMIExperiment object
check4probe

Checks if the probes are available
diffSpliceScore

Calculate differential splice scores
checkDEMIExperiment_pmsize

Checks if pmsize is correct
addCustomTargets

Add new alignments to the alignment table
getAnnotation

Returns the annoTable parameter representing annotation information
demi.wilcox.test.fast

Cluster probes into higher and lower clusters based on their differential signalling
getCelpath

Returns the celpath parameter
demiequal

Cluster probes that have no statistically significant differential signalling
getExperiment

Returns the experiment parameter
getPathway

Returns the pathway parameter representing functional annotation information
getIndexB

Returns the indexB parameter
getTargetProbes

Returns the probe ID's of the specified targets
DEMIDiff

Creates a DEMIDiff object
DEMIResult-class

Class DEMIResult
getName

Returns the name parameter
getResult

Returns the result parameter
attachResult

Attach results from DEMIDiff object to DEMIExperiment object
initialize.DEMIDiff

Initializes the DEMIDiff object
norm.quantile

Quantile normalization function
checkDEMIExperiment_normalization

Checks if normormalization is correct
demisummary

Returns the mean normalized expression levels for the specified targets
getDEMIClust

Returns the cluster parameter
getMaxprobes

Returns the maxprobes parameter
getResultTable

Retruns the DEMI analysis results as a data.frame
loadCytoband

Loads the karyotype information specified by the DEMIExperiment object
getGroupB

Returns the groupB parameter