ResultSet-class: Class ResultSet

In isglobal-brge/MultiDataSet: Implementation of MultiDataSet and ResultSet

Description

Class ResultSet used to encapsulate results from MEAL and omicrexposome.

Usage

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

## S4 method for signature 'ResultSet'
getAssociation(object, rid = 1, coef = 2, contrast = NULL, fNames = NULL, ...)

## 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.labels = TRUE,
  show.effect = FALSE,
  show.lambda = TRUE,
  fNames = c("chromosome", "start"),
  subset,
  highlight,
  ...
)

## 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.labels	(default TRUE) If set to TRUE, features are labelled.
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.
subset	GenomicRanges used to zoom a region in Manhattan plot
highlight	GenomicRanges used to highlight a region in Manhattan plot
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)

• fData: Returns data.frame with feature's data.

• getAssociation: Getter to obtain the raw data.frame from association and integration analysis.

• length: Returns the amoung of analyses stored in the ResultSet.

• names: Returns the names of the omics data used to create the ResultSet.

• opt: Returns a list with the options used to create the ResultSet

• plot: Allows to plot a series of plots (QQ plot, Manhattan plot and Volcano plot) depending on the results stored in the ResultSet.

• varLabels: Returns the names of the variables of the models used in a ResultSet.

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

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

isglobal-brge/MultiDataSet documentation built on Oct. 9, 2021, 11:42 a.m.