A |
Retrieve and set Source S and Mixing matrix A from IcaSet |
A-method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
A<- |
Retrieve and set Source S and Mixing matrix A from IcaSet |
A<--method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
Afile |
Class to contain parameters for the analysis of an ICA decomposition. |
Afile-method |
Class to contain parameters for the analysis of an ICA decomposition. |
Afile<- |
Class to contain parameters for the analysis of an ICA decomposition. |
Afile<--method |
Class to contain parameters for the analysis of an ICA decomposition. |
Alist |
Retrieve sample contributions stored in an 'IcaSet' object as a list. |
Alist-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
annot2col |
Class to contain parameters for the analysis of an ICA decomposition. |
annot2col-method |
Class to contain parameters for the analysis of an ICA decomposition. |
annot2col<- |
Class to contain parameters for the analysis of an ICA decomposition. |
annot2col<--method |
Class to contain parameters for the analysis of an ICA decomposition. |
annot2Color |
Association of a colour with each annotation level |
annotCarbayo |
Carbayo annotation data |
annotFeatures |
Annotation of features using an annotation package |
annotFeaturesComp |
Features annotation |
annotFeaturesWithBiomaRt |
Annotation of features using 'biomaRt' |
annotfile |
Class to contain parameters for the analysis of an ICA decomposition. |
annotfile-method |
Class to contain parameters for the analysis of an ICA decomposition. |
annotfile<- |
Class to contain parameters for the analysis of an ICA decomposition. |
annotfile<--method |
Class to contain parameters for the analysis of an ICA decomposition. |
annotInGene |
Features annotation of an object of class IcaSet. |
annotReciprocal |
annotReciprocal |
chipManu |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
chipManu-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
chipManu<- |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
chipManu<--method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
chipVersion |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
chipVersion-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
chipVersion<- |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
chipVersion<--method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
class:IcaSet |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
class:MineICAParams |
Class to contain parameters for the analysis of an ICA decomposition. |
clusterFastICARuns |
Run of fastICA and JADE algorithms |
clusterSamplesByComp |
Cluster samples from an IcaSet |
clusterSamplesByComp_multiple |
Cluster samples from an IcaSet |
clusVarAnalysis |
Tests association between clusters of samples and variables |
compareAn |
Comparison of IcaSet objects using correlation |
compareAn2graphfile |
compareAn2graphfile |
compareGenes |
Union and intersection of contributing genes |
compNames |
Retrieve and set component labels, indices, and witness genes from IcaSet |
compNames-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
compNames<- |
Retrieve and set component labels, indices, and witness genes from IcaSet |
compNames<--method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
compNames<--method |
Retrieve and set component labels, indices, and witness genes from IcaSet |
cor2An |
Correlation between two matrices |
correl2Comp |
correl2Comp |
dat |
Retrieve and set data from IcaSet |
dat-method |
Retrieve and set data from IcaSet |
dat<- |
Retrieve and set data from IcaSet |
dat<--method |
Retrieve and set data from IcaSet |
dataCarbayo |
Carbayo expression data |
datByGene |
Retrieve and set data from IcaSet |
datByGene-method |
Retrieve and set data from IcaSet |
datByGene<- |
Retrieve and set data from IcaSet |
datByGene<--method |
Retrieve and set data from IcaSet |
datfile |
Class to contain parameters for the analysis of an ICA decomposition. |
datfile-method |
Class to contain parameters for the analysis of an ICA decomposition. |
datfile<- |
Class to contain parameters for the analysis of an ICA decomposition. |
datfile<--method |
Class to contain parameters for the analysis of an ICA decomposition. |
geneNames |
Retrieve and set data from IcaSet |
geneNames-method |
Retrieve and set data from IcaSet |
genesPath |
Class to contain parameters for the analysis of an ICA decomposition. |
genesPath-method |
Class to contain parameters for the analysis of an ICA decomposition. |
genesPath<- |
Class to contain parameters for the analysis of an ICA decomposition. |
genesPath<--method |
Class to contain parameters for the analysis of an ICA decomposition. |
getA |
Retrieve and set Source S and Mixing matrix A from IcaSet |
getA-method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
getAfile |
Class to contain parameters for the analysis of an ICA decomposition. |
getAnnot2col |
Class to contain parameters for the analysis of an ICA decomposition. |
getAnnotfile |
Class to contain parameters for the analysis of an ICA decomposition. |
getChipManu-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
getComp |
Retrieve feature and sample values on a component stored in an 'IcaSet' object. |
getComp,IcaSet,character,numeric |
Retrieve feature and sample values on a component stored in an 'IcaSet' object. |
getComp-method |
Retrieve feature and sample values on a component stored in an 'IcaSet' object. |
getdatfile |
Class to contain parameters for the analysis of an ICA decomposition. |
getGenesPath |
Class to contain parameters for the analysis of an ICA decomposition. |
getIndComp |
Retrieve and set component labels, indices, and witness genes from IcaSet |
getIndComp-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
getLabelsComp |
Retrieve and set component labels, indices, and witness genes from IcaSet |
getLabelsComp-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
getMart-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
getProj |
Extract projection values |
getPvalCutoff |
Class to contain parameters for the analysis of an ICA decomposition. |
getRefSamples-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
getResPath |
Class to contain parameters for the analysis of an ICA decomposition. |
getS |
Retrieve and set Source S and Mixing matrix A from IcaSet |
getS-method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
getSByGene |
Retrieve and set Source S and Mixing matrix A from IcaSet |
getSByGene-method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
getSelCutoff |
Class to contain parameters for the analysis of an ICA decomposition. |
getSfile |
Class to contain parameters for the analysis of an ICA decomposition. |
getTypeID-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
getWitGenes |
Retrieve and set component labels, indices, and witness genes from IcaSet |
IcaSet |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
IcaSet-class |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
icaSetCarbayo |
IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples. |
icaSetKim |
IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples. |
icaSetRiester |
IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples. |
icaSetStransky |
IcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples. |
indComp |
Retrieve and set component labels, indices, and witness genes from IcaSet |
indComp-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
indComp<- |
Retrieve and set component labels, indices, and witness genes from IcaSet |
indComp<--method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
indComp<--method |
Retrieve and set component labels, indices, and witness genes from IcaSet |
refSamples |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
refSamples-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
refSamples<- |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
refSamples<--method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
relativePath |
Relative path |
resPath |
Class to contain parameters for the analysis of an ICA decomposition. |
resPath-method |
Class to contain parameters for the analysis of an ICA decomposition. |
resPath<- |
Class to contain parameters for the analysis of an ICA decomposition. |
resPath<--method |
Class to contain parameters for the analysis of an ICA decomposition. |
runAn |
Run analysis of an IcaSet object |
runCompareIcaSets |
runCompareIcaSets |
runEnrich |
Enrichment analysis through GOstats |
runICA |
Run of fastICA and JADE algorithms |
S |
Retrieve and set Source S and Mixing matrix A from IcaSet |
S-method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
S<- |
Retrieve and set Source S and Mixing matrix A from IcaSet |
S<--method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
SByGene |
Retrieve and set Source S and Mixing matrix A from IcaSet |
SByGene-method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
SByGene<- |
Retrieve and set Source S and Mixing matrix A from IcaSet |
SByGene<--method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
selCutoff |
Class to contain parameters for the analysis of an ICA decomposition. |
selCutoff-method |
Class to contain parameters for the analysis of an ICA decomposition. |
selCutoff<- |
Class to contain parameters for the analysis of an ICA decomposition. |
selCutoff<--method |
Class to contain parameters for the analysis of an ICA decomposition. |
selectContrib |
Select contributing features/genes |
selectContrib,list,numeric,ANY |
Select contributing features/genes |
selectContrib-method |
Select contributing features/genes |
selectFeatures_IQR |
Selection of features based on their IQR |
selectWitnessGenes |
selectWitnessGenes |
setA-method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
setA<- |
Retrieve and set Source S and Mixing matrix A from IcaSet |
setAfile |
Class to contain parameters for the analysis of an ICA decomposition. |
setAnnot2col |
Class to contain parameters for the analysis of an ICA decomposition. |
setAnnotfile |
Class to contain parameters for the analysis of an ICA decomposition. |
setChipManu-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
setdatfile |
Class to contain parameters for the analysis of an ICA decomposition. |
setGenesPath |
Class to contain parameters for the analysis of an ICA decomposition. |
setIndComp |
Retrieve and set component labels, indices, and witness genes from IcaSet |
setIndComp-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
setLabelsComp |
Retrieve and set component labels, indices, and witness genes from IcaSet |
setLabelsComp-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
setMart-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
setPvalCutoff |
Class to contain parameters for the analysis of an ICA decomposition. |
setRefSamples-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
setResPath |
Class to contain parameters for the analysis of an ICA decomposition. |
setS-method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
setS<- |
Retrieve and set Source S and Mixing matrix A from IcaSet |
setSByGene-method |
Retrieve and set Source S and Mixing matrix A from IcaSet |
setSByGene<- |
Retrieve and set Source S and Mixing matrix A from IcaSet |
setSelCutoff |
Class to contain parameters for the analysis of an ICA decomposition. |
setSfile |
Class to contain parameters for the analysis of an ICA decomposition. |
setTypeID-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
setWitGenes |
Retrieve and set component labels, indices, and witness genes from IcaSet |
Sfile |
Class to contain parameters for the analysis of an ICA decomposition. |
Sfile-method |
Class to contain parameters for the analysis of an ICA decomposition. |
Sfile<- |
Class to contain parameters for the analysis of an ICA decomposition. |
Sfile<--method |
Class to contain parameters for the analysis of an ICA decomposition. |
Slist |
Retrieve feature/gene projections stored in an 'IcaSet' object as a list. |
Slist-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |
SlistByGene |
Retrieve feature/gene projections stored in an 'IcaSet' object as a list. |
SlistByGene-method |
Class to Contain and Describe an ICA decomposition of High-Throughput Data. |