translateSampleNames: Translate sample names using translation file

In GeneRegionScan: GeneRegionScan

Description

Function that will change sample names in an ExpressionSet using a translation file.

Usage

    translateSampleNames(object, translationFile, from, to)

Arguments

object	An ExpressionSet
translationFile	Character string with the path to a tab-separated text file with translations of names. Alternatively a data frame containing translation information.
from	Character string with the translationFile column name containing the values to translate from.
to	Character string with the translationFile column name containing the values to translate to.

Details

Function that can translate the sampleNames of an ExpressionSet when given translation information. The translationFile argument gives the translation between sampleNames as they are and the sampleNames as they should be. It can either be a character string with the path to a tab-separated text-file with headers or a directly a data frame with the necessary information. The variables 'from' and 'to' specify the column names that contains the translation information. They must be present in the translationFile and the entries in 'from' must be present in the sampleNames of the current ExpressionSet. Extra entries in the translationFile are omitted but samples in the ExpressionSet without samples in the translationFile will raise an error.

This package is particularly useful after running cel-files through the Affymetrix Power Tools (with getLocalProbeIntensities for example), since this program has a tendency to change any odd character in the filename to something else.

Value

The same ExpressionSet given as argument, but with sampleNames changed as specified in translationFile

Author(s)

Lasse Folkersen

Examples

	data(exampleProbeLevelSet)
	
	fromThese<-sampleNames(exampleProbeLevelSet)
	
	toThese<-sub(".cel","", sampleNames(exampleProbeLevelSet))
	toThese<-sub("X","", toThese)
	

	translationFile<-cbind(fromThese, toThese)
	translationFile<-as.data.frame(translationFile)
	
	translateSampleNames(exampleProbeLevelSet, translationFile, from="fromThese", to="toThese")
				
	

GeneRegionScan documentation built on Nov. 8, 2020, 8:28 p.m.