generics: GEVA Generic Methods

In nunesijg/geva: Gene Expression Variation Analysis (GEVA)

Description

Exhaustive list of generic methods exported from GEVA. Use findMethods to retrieve the specific usages.

Usage

inputvalues(object)

inputweights(object, normalized)

inputdata(object)

inputnames(object)

infolist(object, field, ...)

infolist(object) <- value

factors(object)

factors(object) <- value

classification.table(object)

classification.table(object) <- value

analysis.params(gobject)

featureTable(object)

featureTable(object) <- value

sv(object)

svattr(S, V)

elem.class(typedlist)

elem.class(typedlist) <- value

groupsets(object)

groupsets(object) <- value

groups(object)

scores(object, group)

centroids(object)

offsets(object)

sv.scores(object)

qindexes(object)

qareasizes(object)

qcount(object)

quantiles(object)

quantiles.method(object)

group.rels(object)

cluster.method(object)

results.table(gres)

sv.data(object)

variation(object, ...)

get.summary.method(x)

get.variation.method(x)

get.distance.method(x)

as.SVTable(x, ...)

Arguments

object, x, gobject	Primary object. See the documentation from each class for specific usages
normalized	logical, whether to return values in the normalized scale
field	When used with a information list, returns the information entry with the corresponding name
...	Additional parameters. If used with an imported S3 method, passes the arguments to the default vector, matrix or data.frame implementation
value	The value to be assigned
S	Vector to construct the S slot
V	Vector to construct the V slot
typedlist	A TypedList object
group	Character to filter the returned groups. Omit it to return all groups
gres	A GEVAResults objec

Value

See the specific usages for each method.

Examples

# Returing analysis parameters from an object
gsummary <- geva.summarize(geva.ideal.example(),
                           summary.method="mean",
                           variation.method="sd")
anpars <- analysis.params(gsummary)
print(anpars)
# $summary.method
# [1] "mean"
# $variation.method
# [1] "sd"

nunesijg/geva documentation built on March 12, 2021, 3:58 p.m.