Gene Expression Variation Analysis (GEVA)

---

Documentation for package ‘geva’ version 1.15.0

• 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)