CnvGSAInput-class: Class '"CnvGSAInput"'

In JoeLugo/cnvGSA: Gene Set Analysis of (Rare) Copy Number Variants

Description

Container class for the input structures required by the main function (i.e. cnvGSALogRegTest()).

Slots

config.ls:

Object of class "list" containing the file names and paths.

params.ls:

Object of class "list" containing the test parameters.

cnvData.ls:

Object of class "list" containing CNV data.

phData.ls:

Object of class "list" containing phenotype and covariate data.

gsData.ls:

Object of class "list" containing gene-set data.

geneID.ls:

Object of class "list" containing Gene ID data.

Constructor

CnvGSAInput( config.ls, params.ls, cnvData.ls, phData.ls, gsData.ls, geneID.ls): Creates a CnvGSAInput object.

config.ls

Structure containing the file names and paths.

params.ls

Structure containing main test parameters.

cnvData.ls

Structure containing CNV data along with sample-to-class information and filters.

phData.ls

Structure containing phenotype and covariate data.

gsData.ls

Structure containing gene-set data.

geneID.ls

Structure containing Gene ID data.

See the vignette for complete details on each of these structures as well as a full example of how to load them.

Methods

config.ls

signature(obj = "CnvGSAInput"): Gets config.ls.

config.ls<-

signature(obj = "CnvGSAInput"): Sets config.ls.

params.ls

signature(obj = "CnvGSAInput"): Gets params.ls.

params.ls<-

signature(obj = "CnvGSAInput"): Sets params.ls.

cnvData.ls

signature(obj = "CnvGSAInput"): Gets cnvData.ls.

cnvData.ls<-

signature(obj = "CnvGSAInput"): Sets cnvData.ls.

phData.ls

signature(obj = "CnvGSAInput"): Gets phData.ls.

phData.ls<-

signature(obj = "CnvGSAInput"): Sets phData.ls.

gsData.ls

signature(obj = "CnvGSAInput"): Gets gsData.ls.

gsData.ls<-

signature(obj = "CnvGSAInput"): Sets gsData.ls.

geneID.ls

signature(obj = "CnvGSAInput"): Gets geneID.ls.

geneID.ls<-

signature(obj = "CnvGSAInput"): Sets geneID.ls.

Author(s)

Joseph Lugo [e-mail]

Examples

## See vignette for full details and worked example

JoeLugo/cnvGSA documentation built on May 28, 2019, 12:55 p.m.