MSigDB: Class 'MSigDB'

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

Class MSigDB

Description

This was the class for storing data from MSigDB and analysis results. We now generally recommend using the Create_DEGContainer to create it in DEGContainer obj.

Usage

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Value

The accessor functions msigdbParam, msigdbData, msigdbGSEAparam, msigdbGSEAresult, msigdbGSVAresult return the corresponding elements of a DEGContainer or MSigDB.

Slots

msigdbParam

list_OR_NULL. Store Param of msigdbr

msigdbData

list. Save data download from MSigDB by msigdbr.

msigdbGSEAparam

list_OR_NULL. Store Param of GSEA

msigdbHyperParam

list_OR_NULL. Store Param of enricher

msigdbGSEAresult

list. Store results of GSEA.

msigdbHyperResult

list. Store results of Hyper

msigdbGSVAresult

list. Store results of GSVA.

See Also

Other DEGContainer: dataInfo, degResults-class

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