Gene Expression Variation Analysis (GEVA)


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Documentation for package ‘geva’ version 1.15.0

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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)