# Gene Expression Variation Analysis (GEVA)

## Documentation for package ‘geva’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H I L N O P Q R S T V W misc

## -- A --

analysis.params | GEVA Generic Methods
analysis.params-method | GEVA Grouping Results
analysis.params-method | GEVA Grouped Summary-Variation Table
analysis.params-method | GEVA Input Data
analysis.params-method | GEVA Results Table
analysis.params-method | GEVA Summary-Variation Table
as.array.GEVAInput | GEVA Input Data
as.character.SVAttribute | Summary-Variation Attribute Field
as.data.frame.GEVAGroupSet | GEVA Grouping Results
as.data.frame.SVTable | Summary-Variation Table
as.expression.GEVAGroupedSummary | GEVA Grouped Summary-Variation Table
as.expression.GEVAGroupSet | GEVA Grouping Results
as.expression.GEVAQuantiles | GEVA Quantiles Grouping Results
as.expression.GEVAResults | GEVA Results Table
as.expression.GEVASummary | GEVA Summary-Variation Table
as.list.TypedList | Type-strict List (TypedList-class)
as.matrix.GEVAGroupedSummary | GEVA Grouped Summary-Variation Table
as.matrix.GEVASummary | GEVA Summary-Variation Table
as.matrix.SVTable | Summary-Variation Table
as.SVTable | GEVA Generic Methods
as.SVTable.data.frame | Summary-Variation Table
as.SVTable.GEVAGroupSet | GEVA Grouping Results
as.SVTable.GEVAQuantiles | GEVA Quantiles Grouping Results
as.SVTable.matrix | Summary-Variation Table
as.SVTable.SVTable | Summary-Variation Table
as.typed.list.list | Type-strict List (TypedList-class)
as.typed.list.TypedList | Type-strict List (TypedList-class)
as.typed.list.vector | Type-strict List (TypedList-class)
as.vector.SVAttribute | Summary-Variation Attribute Field

## -- C --

centroids | GEVA Generic Methods
centroids-method | GEVA Grouping Results
classification.table | GEVA Generic Methods
classification.table-method | GEVA Grouping Results
classification.table-method | GEVA Quantiles Grouping Results
classification.table<- | GEVA Generic Methods
classification.table<--method | GEVA Grouping Results
classification.table<--method | GEVA Quantiles Grouping Results
cluster.method | GEVA Generic Methods
cluster.method-method | GEVA Clustering Results
cluster.method-method | GEVA Grouping Results
cluster.method-method | GEVA Grouped Summary-Variation Table
cluster.method-method | GEVA Quantiles Grouping Results
color.values.GEVAGroupSet | GEVA Grouping Results

## -- D --

dim-method | GEVA Input Data
dim-method | GEVA Quantiles Grouping Results
dim-method | GEVA Results Table
dim-method | Summary-Variation Attribute Field
dim-method | Summary-Variation Table
dimnames-method | GEVA Input Data
dimnames-method | GEVA Results Table
dimnames-method | Summary-Variation Table
dimnames<--method | GEVA Input Data

## -- E --

elem.class | GEVA Generic Methods
elem.class-method | Type-strict List (TypedList-class)
elem.class<- | GEVA Generic Methods
elem.class<--method | Type-strict List (TypedList-class)

## -- F --

factors | GEVA Generic Methods
factors-method | GEVA Input Data
factors-method | GEVA Summary-Variation Table
factors<- | GEVA Generic Methods
factors<--method | GEVA Input Data
factors<--method | GEVA Summary-Variation Table
featureTable | GEVA Generic Methods
featureTable-method | GEVA Grouping Results
featureTable-method | GEVA Input Data
featureTable-method | GEVA Results Table
featureTable-method | GEVA Summary-Variation Table
featureTable<- | GEVA Generic Methods
featureTable<--method | GEVA Input Data
format.SVTable | Summary-Variation Table

## -- G --

generics | GEVA Generic Methods
get.distance.method | GEVA Generic Methods
get.summary.method | GEVA Generic Methods
get.summary.method.GEVASummary | GEVA Summary-Variation Table
get.variation.method | GEVA Generic Methods
get.variation.method.GEVASummary | GEVA Summary-Variation Table
geva.cluster | GEVA Cluster Analysis
geva.dcluster | GEVA Density Clustering
geva.finalize | Concatenating GEVA calculations into the final results
geva.hcluster | GEVA Hierarchical Clustering
geva.ideal.example | GEVA "Ideal" Example for Package Testing
geva.input.correct | GEVA Input Post-processing
geva.input.filter | GEVA Input Post-processing
geva.input.rename.rows | GEVA Input Post-processing
geva.merge.input | GEVA Input Processing and Merge
geva.quantiles | GEVA Quantiles Detection
geva.quick | All-In-One Function for GEVA Intermediate Procedures
geva.read.tables | GEVA Input Processing and Merge
geva.summarize | Summarizes the GEVAInput
GEVACluster-class | GEVA Clustering Results
GEVAGroupedSummary-class | GEVA Grouped Summary-Variation Table
GEVAGroupSet-class | GEVA Grouping Results
GEVAInput-class | GEVA Input Data
GEVAQuantiles-class | GEVA Quantiles Grouping Results
GEVAQuantilesAdjusted-class | GEVA Adjusted Quantiles Results
GEVAResults-class | GEVA Results Table
GEVASummary-class | GEVA Summary-Variation Table
group.rels | GEVA Generic Methods
group.rels-method | GEVA Adjusted Quantiles Results
groups | GEVA Generic Methods
groups-method | GEVA Grouping Results
groupsets | GEVA Generic Methods
groupsets-method | GEVA Grouped Summary-Variation Table
groupsets-method | GEVA Summary-Variation Table
groupsets<- | GEVA Generic Methods
groupsets<--method | GEVA Grouped Summary-Variation Table
groupsets<--method | GEVA Summary-Variation Table

## -- H --

head.GEVAInput | GEVA Input Data
head.GEVAResults | GEVA Results Table
head.SVTable | Summary-Variation Table

## -- I --

infolist | GEVA Generic Methods
infolist-method | GEVA Grouping Results
infolist-method | GEVA Input Data
infolist-method | GEVA Results Table
infolist-method | GEVA Summary-Variation Table
infolist<- | GEVA Generic Methods
infolist<--method | GEVA Grouping Results
infolist<--method | GEVA Input Data
infolist<--method | GEVA Summary-Variation Table
inputdata | GEVA Generic Methods
inputdata-method | GEVA Input Data
inputdata-method | GEVA Results Table
inputdata-method | GEVA Summary-Variation Table
inputnames | GEVA Generic Methods
inputnames-method | GEVA Input Data
inputnames-method | GEVA Summary-Variation Table
inputvalues | GEVA Generic Methods
inputvalues-method | GEVA Input Data
inputvalues-method | GEVA Results Table
inputvalues-method | GEVA Summary-Variation Table
inputweights | GEVA Generic Methods
inputweights-method | GEVA Input Data
inputweights-method | GEVA Results Table
inputweights-method | GEVA Summary-Variation Table
is.na.SVTable | Summary-Variation Table

## -- L --

length-method | GEVA Grouping Results
length-method | GEVA Input Data
length-method | GEVA Results Table
length-method | Summary-Variation Table
levels.GEVAGroupSet | GEVA Grouping Results
levels.GEVAInput | GEVA Input Data
levels.GEVAResults | GEVA Results Table
lines.GEVACluster | GEVA Clustering Results
lines.GEVAGroupedSummary | GEVA Grouped Summary-Variation Table
lines.GEVAQuantiles | GEVA Quantiles Grouping Results

## -- N --

names-method | GEVA Grouping Results
names-method | GEVA Input Data
names-method | GEVA Results Table
names-method | Summary-Variation Attribute Field
names-method | Summary-Variation Table

## -- O --

offsets | GEVA Generic Methods
offsets-method | GEVA Grouping Results
options.cl.score.method | GEVA Cluster Analysis
options.cluster.method | GEVA Cluster Analysis
options.dcluster.method | GEVA Density Clustering
options.distance | GEVA Cluster Analysis
options.factoring.p.adjust | Concatenating GEVA calculations into the final results
options.hc.method | GEVA Hierarchical Clustering
options.hc.metric | GEVA Hierarchical Clustering
options.quantiles | GEVA Quantiles Detection
options.summary | Summarizes the GEVAInput
options.variation | Summarizes the GEVAInput

## -- P --

plot-method | GEVA Clustering Results
plot-method | GEVA Grouping Results
plot-method | GEVA Grouped Summary-Variation Table
plot-method | GEVA Input Data
plot-method | GEVA Quantiles Grouping Results
plot-method | GEVA Results Table
plot-method | GEVA Summary-Variation Table
plot-method | Summary-Variation Table
points.GEVAGroupedSummary | GEVA Grouped Summary-Variation Table
points.GEVAGroupSet | GEVA Grouping Results
points.GEVAResults | GEVA Results Table
points.SVTable | Summary-Variation Table

## -- Q --

qareasizes | GEVA Generic Methods
qareasizes-method | GEVA Quantiles Grouping Results
qcount | GEVA Generic Methods
qcount-method | GEVA Quantiles Grouping Results
qindexes | GEVA Generic Methods
qindexes-method | GEVA Quantiles Grouping Results
quantiles | GEVA Generic Methods
quantiles-method | GEVA Grouped Summary-Variation Table
quantiles-method | GEVA Quantiles Grouping Results
quantiles-method | GEVA Results Table
quantiles-method | GEVA Summary-Variation Table
quantiles.method | GEVA Generic Methods
quantiles.method-method | GEVA Quantiles Grouping Results

## -- R --

results.table | GEVA Generic Methods
results.table-method | GEVA Results Table

## -- S --

scores | GEVA Generic Methods
scores-method | GEVA Grouping Results
show-method | GEVA Clustering Results
show-method | GEVA Grouping Results
show-method | GEVA Grouped Summary-Variation Table
show-method | GEVA Input Data
show-method | GEVA Quantiles Grouping Results
show-method | GEVA Adjusted Quantiles Results
show-method | GEVA Results Table
show-method | GEVA Summary-Variation Table
show-method | Summary-Variation Attribute Field
show-method | Summary-Variation Table
show-method | Type-strict List (TypedList-class)
summary.SVAttribute | Summary-Variation Attribute Field
summary.SVTable | Summary-Variation Table
sv | GEVA Generic Methods
sv-method | GEVA Grouping Results
sv-method | GEVA Results Table
sv-method | Summary-Variation Attribute Field
sv-method | Summary-Variation Table
sv.data | GEVA Generic Methods
sv.data-method | GEVA Grouping Results
sv.data-method | GEVA Results Table
sv.data-method | Summary-Variation Attribute Field
sv.data-method | Summary-Variation Table
sv.scores | GEVA Generic Methods
sv.scores-method | GEVA Quantiles Grouping Results
svattr | GEVA Generic Methods
svattr-method | Summary-Variation Attribute Field
SVAttribute | Summary-Variation Attribute Field
SVAttribute-class | Summary-Variation Attribute Field
SVChrAttribute | Summary-Variation Attribute Field
SVChrAttribute-class | Summary-Variation Attribute Field
SVIntAttribute | Summary-Variation Attribute Field
SVIntAttribute-class | Summary-Variation Attribute Field
SVNumAttribute | Summary-Variation Attribute Field
SVNumAttribute-class | Summary-Variation Attribute Field
SVTable | Summary-Variation Table
svtable | Summary-Variation Table
SVTable-class | Summary-Variation Table

## -- T --

tail.GEVAInput | GEVA Input Data
tail.SVTable | Summary-Variation Table
top.genes | Top Results from GEVA
typed.list | Type-strict List (TypedList-class)
TypedList-class | Type-strict List (TypedList-class)

## -- V --

variation | GEVA Generic Methods
variation.SVAttribute | Summary-Variation Attribute Field
variation.SVTable | Summary-Variation Table

## -- W --

with.SVTable | Summary-Variation Table

## -- misc --

$-method | GEVA Results Table
$-method | Summary-Variation Attribute Field
$-method | Summary-Variation Table
[-method | GEVA Input Data
[-method | GEVA Quantiles Grouping Results
[-method | GEVA Results Table
[-method | Summary-Variation Attribute Field
[-method | Summary-Variation Table
[-method | Type-strict List (TypedList-class)
[<--method | Type-strict List (TypedList-class)