API for sbcblab/geva
Gene Expression Variation Analysis (GEVA)

Global functions
$,GEVAResults-method	Man page
$,SVAttribute-method	Man page
$,SVTable-method	Man page
...arg	Source code
...merge	Source code
.onLoad	Source code
GEVACluster-class	Man page
GEVAGroupSet-class	Man page
GEVAGroupedSummary-class	Man page
GEVAInput-class	Man page
GEVAQuantiles-class	Man page
GEVAQuantilesAdjusted-class	Man page
GEVAResults-class	Man page
GEVASummary-class	Man page
SVAttribute	Man page
SVAttribute-class	Man page
SVChrAttribute	Man page
SVChrAttribute-class	Man page
SVIntAttribute	Man page
SVIntAttribute-class	Man page
SVNumAttribute	Man page
SVNumAttribute-class	Man page
SVTable	Man page
SVTable-class	Man page
TypedList-class	Man page
[,GEVAInput,ANY,ANY,ANY-method	Man page
[,GEVAQuantiles,ANY,ANY,ANY-method	Man page
[,GEVAResults,ANY,ANY,ANY-method	Man page
[,SVAttribute,ANY,ANY,ANY-method	Man page
[,SVTable,ANY,ANY,ANY-method	Man page
[,TypedList,ANY,missing,missing-method	Man page
[<-,TypedList,character,missing-method	Man page
`%ifnull%`	Source code
`+`	Source code
all.apply	Source code
analysis.params	Man page
analysis.params,GEVAGroupSet-method	Man page
analysis.params,GEVAGroupedSummary-method	Man page
analysis.params,GEVAInput-method	Man page
analysis.params,GEVAResults-method	Man page
analysis.params,GEVASummary-method	Man page
any.apply	Source code
append.groupsets	Source code
as.SVTable	Man page Source code
as.SVTable.GEVAGroupSet	Man page Source code
as.SVTable.GEVAQuantiles	Man page Source code
as.SVTable.SVTable	Man page Source code
as.SVTable.data.frame	Man page Source code
as.SVTable.matrix	Man page Source code
as.array.GEVAInput	Man page Source code
as.character.SVAttribute	Man page Source code
as.data.frame.GEVAGroupSet	Man page Source code
as.data.frame.SVTable	Man page Source code
as.expression.GEVAGroupSet	Man page Source code
as.expression.GEVAGroupedSummary	Man page Source code
as.expression.GEVAQuantiles	Man page Source code
as.expression.GEVAResults	Man page Source code
as.expression.GEVASummary	Man page Source code
as.list.TypedList	Man page Source code
as.matrix.GEVAGroupedSummary	Man page Source code
as.matrix.GEVASummary	Man page Source code
as.matrix.SVTable	Man page Source code
as.typed.list	Source code
as.typed.list.TypedList	Man page Source code
as.typed.list.list	Man page Source code
as.typed.list.vector	Man page Source code
as.vector.SVAttribute	Man page Source code
assert.callres	Source code
assert.choices	Source code
assert.class	Source code
assert.dim	Source code
assert.included	Source code
assert.names.equal	Source code
assert.notempty	Source code
assert.operator	Source code
basename_noext	Source code
calc.cluster.centroids	Source code
calc.cluster.offsets	Source code
calc.cluster.scores	Source code
calc.cluster.scores.centroid	Source code
calc.cluster.scores.density	Source code
calc.cluster.scores.hclust.height	Source code
calc.dclust.knnd	Source code
calc.eps.from.resolution	Source code
calc.hclust.tree	Source code
calc.inbetweens	Source code
calc.quantile.centroids	Source code
calc.quantile.indexes	Source code
calc.quantile.initial.threshold	Source code
calc.quantile.nearest.SVTable	Source code
calc.quantile.nearest.sindex	Source code
calc.quantile.nearest.vector	Source code
calc.quantile.thresholds	Source code
call.arg.characters	Source code
call.default.arg	Source code
call.dots.argnames	Source code
call.dots.args	Source code
call.dots.asis	Source code
call.dots.named.list	Source code
call.dots.namesorargs	Source code
call.dots.which.frame	Source code
call.objname	Source code
call.plot	Source code
catline	Source code
centroids	Man page
centroids,GEVAGroupSet-method	Man page
check.factors.are.specific	Source code
check.quantiles.count	Source code
check.suitable.factors	Source code
check.typed.list.class	Source code
clamp	Source code
classification.table	Man page
classification.table,GEVAGroupSet-method	Man page
classification.table,GEVAQuantiles-method	Man page
classification.table<-	Man page
classification.table<-,GEVAGroupSet,data.frame-method	Man page
classification.table<-,GEVAQuantiles,data.frame-method	Man page
clean_calls	Source code
cluster.method	Man page
cluster.method,GEVACluster-method	Man page
cluster.method,GEVAGroupSet-method	Man page
cluster.method,GEVAGroupedSummary-method	Man page
cluster.method,GEVAQuantiles-method	Man page
color.adjust	Source code
color.values	Source code
color.values.GEVAGroupSet	Man page Source code
color.values.factor	Source code
color.values.vector	Source code
current.class.slots	Source code
dim,GEVAInput-method	Man page
dim,GEVAQuantiles-method	Man page
dim,GEVAResults-method	Man page
dim,SVAttribute-method	Man page
dim,SVTable-method	Man page
dimnames,GEVAInput-method	Man page
dimnames,GEVAResults-method	Man page
dimnames,SVTable-method	Man page
dimnames<-,GEVAInput,list-method	Man page
distinct	Source code
distinct.default	Source code
distinct.formula	Source code
elem.class	Man page
elem.class,TypedList-method	Man page
elem.class<-	Man page
elem.class<-,TypedList,character-method	Man page
factoring.combine.spec.classif	Source code
factoring.dep.fisher	Source code
factoring.init.cltable	Source code
factoring.pval.adjust	Source code
factoring.silhouette.partial.quantiles	Source code
factoring.spec.fisher	Source code
factoring.spec.levene	Source code
factoring.table.spec	Source code
factors	Man page
factors,GEVAInput-method	Man page
factors,GEVASummary-method	Man page
factors<-	Man page
factors<-,GEVAInput,character-method	Man page
factors<-,GEVAInput,factor-method	Man page
factors<-,GEVASummary,character-method	Man page
factors<-,GEVASummary,factor-method	Man page
featureTable	Man page
featureTable,GEVAGroupSet-method	Man page
featureTable,GEVAInput-method	Man page
featureTable,GEVAResults-method	Man page
featureTable,GEVASummary-method	Man page
featureTable<-	Man page
featureTable<-,GEVAInput,data.frame-method	Man page
filter.plotargs	Source code
first	Source code
first.default	Source code
first.formula	Source code
fmt.limit	Source code
format.SVTable	Man page Source code
format.rd_section_methods	Source code
formula2function	Source code
function2expression	Source code
generate.colors	Source code
generate.colors.byfactor	Source code
generate.quantile.colors	Source code
generics	Man page
get.distance.method	Man page Source code
get.distance.method.character	Source code
get.initialized	Source code
get.quantiles.default.classification	Source code
get.summary.method	Man page Source code
get.summary.method.GEVASummary	Man page Source code
get.summary.method.character	Source code
get.variation.method	Man page Source code
get.variation.method.GEVASummary	Man page Source code
get.variation.method.character	Source code
geva	Man page
geva-package	Man page
geva.cluster	Man page Source code
geva.dcluster	Man page Source code
geva.factoring	Source code
geva.finalize	Man page Source code
geva.hcluster	Man page Source code
geva.ideal.example	Man page Source code
geva.input.correct	Man page Source code
geva.input.filter	Man page Source code
geva.input.rename.rows	Man page Source code
geva.merge.input	Man page Source code
geva.quantiles	Man page Source code
geva.quick	Man page Source code
geva.read.tables	Man page Source code
geva.summarize	Man page Source code
group.rels	Man page
group.rels,GEVAQuantilesAdjusted-method	Man page
groups	Man page
groups,GEVAGroupSet-method	Man page
groupsets	Man page
groupsets,GEVAGroupedSummary-method	Man page
groupsets,GEVASummary-method	Man page
groupsets<-	Man page
groupsets<-,GEVAGroupedSummary,GEVAGroupSet-method	Man page
groupsets<-,GEVASummary,GEVAGroupSet-method	Man page
groupsets<-,GEVASummary,TypedList-method	Man page
gtapply	Source code
head.GEVAInput	Man page Source code
head.GEVAResults	Man page Source code
head.SVTable	Man page Source code
headtail	Source code
headtail.data.frame	Source code
headtail.default	Source code
headtail.matrix	Source code
hull.lines	Source code
indexes.headtail	Source code
infolist	Man page
infolist,GEVAGroupSet,character-method	Man page
infolist,GEVAGroupSet,missing-method	Man page
infolist,GEVAInput,character-method	Man page
infolist,GEVAInput,missing-method	Man page
infolist,GEVAResults,character-method	Man page
infolist,GEVAResults,missing-method	Man page
infolist,GEVASummary,missing-method	Man page
infolist<-	Man page
infolist<-,GEVAGroupSet,list-method	Man page
infolist<-,GEVAInput,list-method	Man page
infolist<-,GEVASummary,list-method	Man page
initialize.class.args	Source code
inputdata	Man page
inputdata,GEVAInput-method	Man page
inputdata,GEVAResults-method	Man page
inputdata,GEVASummary-method	Man page
inputnames	Man page
inputnames,GEVAInput-method	Man page
inputnames,GEVASummary-method	Man page
inputvalues	Man page
inputvalues,GEVAInput-method	Man page
inputvalues,GEVAResults-method	Man page
inputvalues,GEVASummary-method	Man page
inputweights	Man page
inputweights,GEVAInput,logical-method	Man page
inputweights,GEVAInput,missing-method	Man page
inputweights,GEVAResults,logical-method	Man page
inputweights,GEVAResults,missing-method	Man page
inputweights,GEVASummary,logical-method	Man page
inputweights,GEVASummary,missing-method	Man page
insert.function.optargs	Source code
is.na.SVTable	Man page Source code
is.named	Source code
is.unitialized	Source code
is.verbose	Source code
isS3implemented	Source code
k.neighbors	Source code
length,GEVAGroupSet-method	Man page
length,GEVAInput-method	Man page
length,GEVAResults-method	Man page
length,SVTable-method	Man page
levels.GEVAGroupSet	Man page Source code
levels.GEVAInput	Man page Source code
levels.GEVAResults	Man page Source code
lines.GEVACluster	Man page Source code
lines.GEVAGroupedSummary	Man page Source code
lines.GEVAQuantiles	Man page Source code
list.flatten	Source code
list.merge	Source code
merge.rd_section_methods	Source code
mrapply	Source code
na.replace	Source code
names,GEVAGroupSet-method	Man page
names,GEVAInput-method	Man page
names,GEVAResults-method	Man page
names,SVAttribute-method	Man page
names,SVTable-method	Man page
normalize.scale	Source code
normalize.scale.numeric	Source code
normalize.weights	Source code
offsets	Man page
offsets,GEVAGroupSet-method	Man page
options.cl.score.method	Man page
options.cluster.method	Man page
options.dcluster.method	Man page
options.distance	Man page
options.factoring.p.adjust	Man page
options.hc.method	Man page
options.hc.metric	Man page
options.quantiles	Man page
options.summary	Man page
options.variation	Man page
orderby.occur	Source code
plot,GEVACluster,SVTable-method	Man page
plot,GEVAGroupSet,GEVAGroupSet-method	Man page
plot,GEVAGroupSet,SVTable-method	Man page
plot,GEVAGroupSet,missing-method	Man page
plot,GEVAGroupedSummary,missing-method	Man page
plot,GEVAInput,missing-method	Man page
plot,GEVAQuantiles,SVTable-method	Man page
plot,GEVAResults,missing-method	Man page
plot,GEVASummary,missing-method	Man page
plot,SVTable,GEVAGroupSet-method	Man page
plot,SVTable,missing-method	Man page
plotargs.sv.proportional	Source code
points.GEVAGroupSet	Man page Source code
points.GEVAGroupedSummary	Man page Source code
points.GEVAResults	Man page Source code
points.SVTable	Man page Source code
promote.class	Source code
qareasizes	Man page
qareasizes,GEVAQuantiles-method	Man page
qcount	Man page
qcount,GEVAQuantiles-method	Man page
qindex2label	Source code
qindexes	Man page
qindexes,GEVAQuantiles-method	Man page
qthreshold.density	Source code
qthreshold.k.max.sd	Source code
qthreshold.proportional	Source code
qthreshold.range.slice	Source code
quantiles	Man page
quantiles,GEVAGroupedSummary-method	Man page
quantiles,GEVAQuantiles-method	Man page
quantiles,GEVAResults-method	Man page
quantiles,GEVASummary-method	Man page
quantiles.assoc.gset	Source code
quantiles.method	Man page
quantiles.method,GEVAQuantiles-method	Man page
quantiles.scores.merge	Source code
restore.weights.pvals	Source code
results.table	Man page
results.table,GEVAResults-method	Man page
results.table.from.classif	Source code
rgauss	Source code
row.factor.sindex.silhouette	Source code
row.factor.sindex.similarity.score	Source code
row.lm.wfit	Source code
row.model.matrix	Source code
row.wanova	Source code
rows.normalize.weights	Source code
rows.weighted.summary	Source code
rows.weighted.variation	Source code
roxy_tag_parse.roxy_tag_category	Source code
roxy_tag_parse.roxy_tag_methodsnote	Source code
roxy_tag_parse.roxy_tag_options	Source code
roxy_tag_parse.roxy_tag_s3method	Source code
roxy_tag_parse.roxy_tag_s3methodDescription	Source code
roxy_tag_parse.roxy_tag_s4accessor	Source code
roxy_tag_parse.roxy_tag_s4method	Source code
roxy_tag_parse.roxy_tag_s4methodDescription	Source code
roxy_tag_rd.roxy_tag_methodsnote	Source code
roxy_tag_rd.roxy_tag_s4methodDescription	Source code
score.plot	Source code
scores	Man page
scores,GEVAGroupSet,character-method	Man page
scores,GEVAGroupSet,missing-method	Man page
show,GEVACluster-method	Man page
show,GEVAGroupSet-method	Man page
show,GEVAGroupedSummary-method	Man page
show,GEVAInput-method	Man page
show,GEVAQuantiles-method	Man page
show,GEVAQuantilesAdjusted-method	Man page
show,GEVAResults-method	Man page
show,GEVASummary-method	Man page
show,SVAttribute-method	Man page
show,SVTable-method	Man page
show,TypedList-method	Man page
sortby.occur	Source code
strconjunct	Source code
strjoin	Source code
summary.SVAttribute	Man page Source code
summary.SVTable	Man page Source code
sv	Man page
sv,GEVAGroupSet-method	Man page
sv,GEVAResults-method	Man page
sv,SVAttribute-method	Man page
sv,SVTable-method	Man page
sv.data	Man page
sv.data,GEVAGroupSet-method	Man page
sv.data,GEVAResults-method	Man page
sv.data,SVAttribute-method	Man page
sv.data,SVTable-method	Man page
sv.scores	Man page
sv.scores,GEVAQuantiles-method	Man page
svattr	Man page
svattr,character,character-method	Man page
svattr,integer,integer-method	Man page
svattr,numeric,numeric-method	Man page
svtable	Man page Source code
tail.GEVAInput	Man page Source code
tail.SVTable	Man page Source code
top.genes	Man page Source code
typed.list	Man page Source code
variation	Man page Source code
variation.SVAttribute	Man page Source code
variation.SVTable	Man page Source code
vars.formula	Source code
vprint	Source code
weighted.sd	Source code
weighted.var	Source code
where	Source code
where.default	Source code
where.formula	Source code
which.outliers	Source code
which.rows.outside.cutoff	Source code
which.slice	Source code
with.GEVAResults	Source code
with.SVTable	Man page Source code