MEAL (version 1.2.3)

AnalysisResults: AnalysisResults instances

Description

Container with the results of per probe and per region analyses.

Usage

analysisResults(set, model, regionResults, probeResults, num_feat = 50, num_vars = ncol(pData(set)))
"blocks"(object)
"bumps"(object)
"covariableNames"(object)
"dmrCate"(object)
"feats"(object)
"featvals"(object)
"getGeneVals"(object, gene)
"getMs"(object, threshold = 1e-04)
"model"(object)
"modelVariables"(object)
"phenoData"(object)
"phenoData"(object) <- value
"pData"(object)
"pData"(object) <- value
"probeResults"(object, drop = TRUE)
"regionResults"(object)
"sampleNames"(object)
"variableNames"(object)
"exportResults"(object, dir = "./", prefix = NULL, vars = modelVariables(object))
"plotEWAS"(object, variable = modelVariables(object)[1], range = NULL)
"plotQQ"(object, variable = modelVariables(object)[1])
"plotRegion"(object, variable = modelVariables(object)[[1]], range = NULL)
"plotVolcano"(object, variable = modelVariables(object)[1], mindiff = NULL)

Arguments

set

MethylationSet or ExpressionSet used to perform the analysis

model

Model matrix used to produce the calculations

regionResults

List with the region results

probeResults

List with the probe results

num_feat

Numeric with the minimum number of feature values to be included.

num_vars

Numeric with the number of columns of the pData table that should be considered as variables.

object

AnalysisResults

gene

Character with the name of the gene

threshold

Numeric with the threshold to avoid 0s and 1s.

value

AnnotatedDataFrame or data.frame with the phenotype

drop

Logical. If TRUE, a data.frame is returned when the list of results contains one element,

dir

Character with the path to export.

prefix

Character with a prefix to be added to all file names.

vars

Character vector with the names of the variables to be exported. Note: names should be that of the model.

variable

Character with the variable name used to obtain the probe results. Note: model name should be used. Original variable name might not be valid.

range

GenomicRange whose probes will be highlighted

mindiff

Numeric with the threshold to consider a difference in methylation or expression significant.

Value

AnalysisResults

Methods (by generic)

• blocks: Get BlockFinder analysis results
• bumps: Get Bumphunter analysis results
• covariableNames: Get covariable names
• dmrCate: Get dmrCate analysis results
• feats: Get features names
• featvals: Get features values matrix
• getGeneVals: Get probe results of a gene
• getMs: Get Ms values
• model: Get model used to perform the analysis
• modelVariables: Get names of the variables in the model matrix
• phenoData: Get phenotypes data (AnnotatedDataFrame)
• phenoData<-: Set phenotypes data (AnnotatedDataFrame)
• pData: Get phenotypes data (data.frame)
• pData<-: Set phenotypes data (data.frame)
• probeResults: Get per probe analysis results
• regionResults: Get all per region analysis results
• sampleNames: Get sample names
• variableNames: Get variable names
• exportResults: Exports results data.frames to csv files.
• plotEWAS: Plot a Manhattan plot with the probe results
• plotQQ: QQ plot of probe analysis
• plotRegion: Plot of the region
• plotVolcano: Make a Volcano plot with the probe results

Slots

originalclass

Character with the class of the object used to perform the analysis

features

Matrix with the values of the most significant features.

phenotypes

AnnotatedDataFrame with the phenotypes.

model

Matrix with the model used in the analysis

sampleNames

Character vector with the names of the samples

variableNames

Character vector with the names of the variables used in the analysis. Names are equal to those find in phenotypes.

covariableNames

Character vector with the names of the covariables used in the analysis. Names are equal to those find in phenotypes.

results

List of data.frames with the results of per probe analysis. Names are those of the model.

DMRcate

List of data.frames with the results of DMRcate. Names are those of the model.

Bumphunter

List of data.frames with the results of Bumphunter. Names are those of the model.

BlockFinder

List of data.frames with the results of BlockFinder. Names are those of the model.

Examples

showClass("AnalysisResults")