A function for creating a factor from the phenoData slot of an exprSet

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Description

This function creates a factor whose levels represent the different classes for a classification problem. It is derived from the column specified in the argument class.column. If the factor has more than two levels, the argument reference.class can be used to transform this into a two-class problem: reference class versus the rest.

Usage

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class.factor.format(x, class.column, reference.class=NULL)

Arguments

x

an exprSet

class.column

either a number or a character string specifying the relevant column of the phenoData slot in x

reference.class

character vector. If specified the result will be a factor with only 2 levels: the reference class(es) versus all other

Value

A factor of length nrow(pData(x))

Author(s)

Markus Ruschhaupt mailto:m.ruschhaupt@dkfz.de

Examples

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 library(golubEsets)
data(Golub_Train)
class.factor.format(Golub_Train[,28:35], "FAB",reference="M1")