proteomicsExprsData {clippda}R Documentation

A generic fuction to extract duplicate SELDI data from an object of aclinicalProteomicsData class in the same format as the data from Biomarkers wizard

Description

This generic function extracts a matrix of duplicate SELDI data from an object of aclinicalProteomicsData class. It then converts it into a dataframe which is in the same format as the data from Biomarkers wizard. In this dataframe, the intensities and the subject mass-to-charge ratio are represented as numeric variables, while the sample-tag is represented as a character variable.

Usage

proteomicsExprsData(Data, ...)

Arguments

Data

is an object of a aclinicalProteomicsData class.

...

means other defined arguments. Currently, we have not defined additional arguments.

Value

A dataframe of expression values, the substance mass, patient labels, and any other defined sample information.

Author(s)

S Nyangoma

Examples

data(liverdata)

data(liver_pheno)

OBJECT=new("aclinicalProteomicsData")

OBJECT@rawSELDIdata=as.matrix(liverdata)
OBJECT@covariates=c("tumor" ,    "sex")
OBJECT@phenotypicData=as.matrix(liver_pheno)
OBJECT@variableClass=c('numeric','factor','factor')
OBJECT@no.peaks=53

head(proteomicsExprsData(OBJECT))
[Package clippda version 1.32.0 Index]