Nothing
##########################################################################
#gsAnalysis
#
# method to define a "gsAnalysis"
##########################################################################
gsAnalysis <- function(
name,
gls = NULL,
glsParameterNames = NULL,
transformation = NULL,
transformationParameterNames = NULL,
gss = NULL,
gssParameterNames = NULL,
globalStat = NULL,
globalStatParameterNames = NULL,
significance = NULL,
significanceParameterNames = NULL,
testAlternative = c("greater", "less")){
analysis <- list(
name = name,
gls = gls,
glsParameterNames = glsParameterNames,
transformation = transformation,
transformationParameterNames = transformationParameterNames,
gss = gss,
gssParameterNames = gssParameterNames,
globalStat = globalStat,
globalStatParameterNames = globalStatParameterNames,
significance = significance,
significanceParameterNames = significanceParameterNames,
testAlternative = testAlternative)
class(analysis) <- "gsAnalysis"
return(analysis)
}
##########################################################################
#print.gsAnalysis
##########################################################################
print.gsAnalysis <- function(x, ...){
cat(x$name, "\n")
if(is.null(x$globalStat)){
cat("Gene level statistic: ", x$gls,
"\n (parameters: ",
paste(x$glsParameterNames,collapse=","),")\n", sep="")
cat("Transformation: ", x$transformation,
"\n (parameters: ",
paste(x$transformationParameterNames,collapse=","),")\n", sep="")
cat("Gene set statistic: ", x$gss,
"\n (parameters: ",
paste(x$gssParameterNames,collapse=","),")\n", sep="")
cat("Significance assessment: ", x$significance,
"\n (parameters: ",
paste(x$significanceParameterNames,collapse=","),")\n", sep="")
cat("Test alternative: ", x$testAlternative, "\n", sep ="")
}else{
cat("Global analysis: ", x$globalStat,
"\n (parameters: ",
paste(x$globalStatParameterNames,collapse=","),")\n", sep="")
}
}
##########################################################################
# Gene Set Enrichment Analysis: Subramanian et al. 2005
##########################################################################
analysis.gsea <- function(){
return(gsAnalysis(
name = "gsea",
gls = "gls.cor",
glsParameterNames = c("labs","method"),
transformation = "transformation.abs",
transformationParameterNames = NULL,
gss = "gss.enrichmentScore",
gssParameterNames = c("p"),
globalStat = NULL,
globalStatParameterNames = NULL,
significance = "significance.permutation",
significanceParameterNames = c("numSamples","labs"),
testAlternative = "greater"))
}
##########################################################################
# Fisher exact test for 2 sets of genes (coreset and geneset)
##########################################################################
analysis.customOverrepresentation <- function(){
return(gsAnalysis(
name = "overrepresentation",
gls = NULL,
glsParameterNames = NULL,
transformation = NULL,
transformationParameterNames = NULL,
gss = NULL,
gssParameterNames = NULL,
globalStat = "global.overrepresentation",
globalStatParameterNames = c("coreSet"),
significance = NULL,
significanceParameterNames = NULL,
testAlternative = NULL))
}
analysis.overrepresentation <- function(){
return(gsAnalysis(
name = "overrepresentation",
gls = "gls.tStatistic",
glsParameterNames = c("pValue", "alternative", "labs"),
transformation = "transformation.adjustAndBinarize",
transformationParameterNames = c("adjMethod", "threshold"),
gss = "gss.fisherExactTest",
gssParameterNames = NULL,
globalStat = NULL,
globalStatParameterNames = NULL,
significance = NULL,
significanceParameterNames = NULL,
testAlternative = NULL))
}
##########################################################################
#Enrichment analyses sample gls -> transformation -> gss -> significance Assessment:
#test correlation, abs.value, ar.meam and sampling
##########################################################################
analysis.averageCorrelation <- function(){
return(gsAnalysis(
name = "averageCorrelation",
gls = "gls.cor",
glsParameterNames = c("labs","method"),
transformation = "transformation.abs",
transformationParameterNames = NULL,
gss = "gss.mean",
gssParameterNames = NULL,
globalStat = NULL,
globalStatParameterNames = NULL,
significance = "significance.sampling",
significanceParameterNames = c("numSamples"),
testAlternative = "greater"))
}
##########################################################################
#Enrichment analyses sample gls -> transformation -> gss -> significance Assessment:
#test t.statistic, abs.value, ar.mean and sampling
##########################################################################
analysis.averageTStatistic <- function(){
return(gsAnalysis(
name = "averageTStatistic",
gls = "gls.tStatistic",
glsParameterNames = c("labs", "pValue", "alternative"),
transformation = "transformation.abs",
transformationParameterNames = NULL,
gss = "gss.mean",
gssParameterNames = NULL,
globalStat = NULL,
globalStatParameterNames = NULL,
significance = "significance.sampling",
significanceParameterNames = c("numSamples"),
testAlternative = "greater"))
}
##########################################################################
#global test: Goeman 2006
##########################################################################
analysis.globalTest <- function(){
return(gsAnalysis(
name = "globalTest",
gls = NULL,
glsParameterNames = NULL,
transformation = NULL,
transformationParameterNames = NULL,
gss = NULL,
gssParameterNames = NULL,
globalStat = "global.test",
globalStatParameterNames = c("response"),
significance = NULL,
significanceParameterNames = NULL,
testAlternative = NULL))
}
##########################################################################
#global ANCOVA: Hummel 2008
##########################################################################
analysis.globalAncova <- function(){
return(gsAnalysis(
name = "globalAncova",
gls = NULL,
glsParameterNames = NULL,
transformation = NULL,
transformationParameterNames = NULL,
gss = NULL,
gssParameterNames = NULL,
globalStat = "global.ancova",
globalStatParameterNames = c("group"),
significance = NULL,
significanceParameterNames = NULL,
testAlternative = NULL))
}
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