DEGContainer: Class 'DEGContainer'

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

Class DEGContainer

Description

This was the universal class for storing data and results. We now generally reommend using the Create_DEGContainer to create it.

Usage

## S4 replacement method for signature 'DEGContainer'
species(obj) <- value

## S4 replacement method for signature 'DEGContainer'
dataType(obj) <- value

## S4 replacement method for signature 'DEGContainer'
idType(obj) <- value

## S4 replacement method for signature 'DEGContainer'
expMatrix(obj) <- value

## S4 replacement method for signature 'DEGContainer'
groupInfo(obj) <- value

## S4 replacement method for signature 'DEGContainer'
caseGroup(obj) <- value

## S4 replacement method for signature 'DEGContainer'
filterMethod(obj) <- value

## S4 replacement method for signature 'DEGContainer'
matrixFiltered(obj) <- value

## S4 replacement method for signature 'DEGContainer'
geneNames(obj, filtered = FALSE) <- value

## S4 replacement method for signature 'DEGContainer'
sampleNames(obj, filtered = FALSE) <- value

## S4 method for signature 'DEGContainer'
treatInfo(obj)

## S4 method for signature 'DEGContainer'
label(obj)

## S4 method for signature 'DEGContainer'
label_ns(obj)

## S4 method for signature 'DEGContainer'
cutFC(obj)

## S4 method for signature 'DEGContainer'
cutFDR(obj)

## S4 method for signature 'DEGContainer'
sigCol(obj)

## S4 method for signature 'DEGContainer'
sigAlpha(obj)

## S4 method for signature 'DEGContainer'
sigSize(obj)

## S4 method for signature 'DEGContainer'
sigShape(obj)

## S4 replacement method for signature 'DEGContainer'
treatInfo(obj) <- value

## S4 replacement method for signature 'DEGContainer'
cutFC(obj) <- value

## S4 replacement method for signature 'DEGContainer'
cutFDR(obj) <- value

## S4 replacement method for signature 'DEGContainer'
label(obj) <- value

## S4 replacement method for signature 'DEGContainer'
label_ns(obj) <- value

## S4 replacement method for signature 'DEGContainer'
sigCol(obj) <- value

## S4 replacement method for signature 'DEGContainer'
sigAlpha(obj) <- value

## S4 replacement method for signature 'DEGContainer'
sigSize(obj) <- value

## S4 replacement method for signature 'DEGContainer'
sigShape(obj) <- value

## S4 method for signature 'DEGContainer'
vsData(obj)

## S4 method for signature 'DEGContainer'
limma_res(obj)

## S4 method for signature 'DEGContainer'
edgeR_res(obj)

## S4 method for signature 'DEGContainer'
DESeq2_res(obj)

## S4 method for signature 'DEGContainer'
merge_res(obj)

## S4 replacement method for signature 'DEGContainer'
vsData(obj) <- value

## S4 replacement method for signature 'DEGContainer'
DESeq2_res(obj) <- value

## S4 replacement method for signature 'DEGContainer'
limma_res(obj) <- value

## S4 replacement method for signature 'DEGContainer'
edgeR_res(obj) <- value

## S4 replacement method for signature 'DEGContainer'
merge_res(obj) <- value

## S4 method for signature 'DEGContainer'
hyperKEGGparam(obj)

## S4 replacement method for signature 'DEGContainer'
hyperKEGGparam(obj) <- value

## S4 method for signature 'DEGContainer'
hyperGOparam(obj)

## S4 replacement method for signature 'DEGContainer'
hyperGOparam(obj) <- value

## S4 method for signature 'DEGContainer'
hyperRes(obj)

## S4 replacement method for signature 'DEGContainer'
hyperRes(obj) <- value

## S4 method for signature 'DEGContainer'
gseKEGGparam(obj)

## S4 replacement method for signature 'DEGContainer'
gseKEGGparam(obj) <- value

## S4 method for signature 'DEGContainer'
gseGOparam(obj)

## S4 replacement method for signature 'DEGContainer'
gseGOparam(obj) <- value

## S4 method for signature 'DEGContainer'
gseRes(obj)

## S4 replacement method for signature 'DEGContainer'
gseRes(obj) <- value

## S4 method for signature 'DEGContainer'
msigdbParam(obj)

## S4 method for signature 'DEGContainer'
msigdbGSEAparam(obj)

## S4 method for signature 'DEGContainer'
msigdbHyperParam(obj)

## S4 replacement method for signature 'DEGContainer'
msigdbParam(obj) <- value

## S4 replacement method for signature 'DEGContainer'
msigdbGSEAparam(obj) <- value

## S4 replacement method for signature 'DEGContainer'
msigdbHyperParam(obj) <- value

## S4 method for signature 'DEGContainer'
msigdbData(obj)

## S4 replacement method for signature 'DEGContainer'
msigdbData(obj) <- value

## S4 method for signature 'DEGContainer'
msigdbGSEAresult(obj)

## S4 replacement method for signature 'DEGContainer'
msigdbGSEAresult(obj) <- value

## S4 method for signature 'DEGContainer'
msigdbHyperResult(obj)

## S4 replacement method for signature 'DEGContainer'
msigdbHyperResult(obj) <- value

## S4 method for signature 'DEGContainer'
msigdbGSVAresult(obj)

## S4 replacement method for signature 'DEGContainer'
msigdbGSVAresult(obj) <- value

## S4 method for signature 'DEGContainer'
msigdbTreat(obj)

## S4 replacement method for signature 'DEGContainer'
msigdbTreat(obj) <- value

Value

The accessor functions dataInfo, degResults, hyperResults, gseResults, MSigDB return the corresponding elements of a DEGContainer.

Slots

dataInfo

store input data of workflow

degResults

store parameters and results in runDEG module

hyperResults

store parameters and results in runHyper module

gseResults

store parameters and results in runGSEA module

MSigDB

store parameters and results in runMSigDB module

xiayh17/RNAseqStat2 documentation built on May 27, 2023, 12:13 p.m.