ResultSet-class: Class ResultSet

Description Usage Arguments Value Methods (by generic) Slots Examples

Description

Class ResultSet used to encapsulate results from MEAL and omicrexposome.

Usage

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## S4 method for signature 'ResultSet'
fData(object)

## S4 method for signature 'ResultSet'
getAssociation(object, rid, coef = 2, contrast = NULL,
  fNames = c("chromosome", "start", "end", "genesymbol"), ...)

## S4 method for signature 'ResultSet'
length(x)

## S4 method for signature 'ResultSet'
names(x)

## S4 method for signature 'ResultSet'
opt(object)

## S4 method for signature 'ResultSet,ANY'
plot(x, y, rid = 1, coef = 2, contrast = NULL,
  type, tFC = 2, tPV = -log10(0.001), show.effect = FALSE,
  show.lambda = TRUE, fNames = c("chromosome", "start"), ...)

## S4 method for signature 'ResultSet'
varLabels(object)

create_resultset(fOrigin, lResults, fData, lOptions = list())

Arguments

object

A ResultSet object.

rid

Name or index of the internal result to be used

coef

Coefficient to be returne, usually 2

contrast

Numeric matrix with the contrasts used to perform the analyses

fNames

Character vector with the names of the fData columns that will be added to the results data.frame.

...

Further arguments passed to topTable

x

A ResultSet object.

y

-

type

Type of plot to be drawn

tFC

Threshold for log FC of effect

tPV

Threshold for P-Value

show.effect

(default: TRUE). Used in volcano plot. If TRUE, effect is shown as FC instead of logFC.

show.lambda

(default: TRUE) If TRUE shows lambda score for the given model.

fOrigin

Chracter with the function used to run the analysis.

lResults

List with the results

fData

List with the feature data.

lOptions

List with additional options

Value

An object of class ResultSet

Methods (by generic)

Slots

fun_origin

Character containing the function that creates the object.

results

List containing the results of the association/integration.

fData

List containing the feature-data of the original objects.

options

list of options used to create the ResultSet.

Examples

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create_resultset("hello", list(), list(), list())

Bioconductor-mirror/MultiDataSet documentation built on June 26, 2017, 10:25 p.m.