vignette.R
In GSALightning: Fast Permutation-based Gene Set Analysis

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(cache=TRUE)

## ----eval = FALSE-------------------------------------------------------------
#  library(devtools)
#  install_github("billyhw/GSALightning")

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library(GSALightning)

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data(expression)
data(sampleInfo)

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data(targetGenes)

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expression <- expression[apply(expression,1,sd) != 0,]

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GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, 
		   		   	       nperm = 1000, minsize = 10, rmGSGenes = 'gene')
head(GSALightResults)

## ----eval=FALSE---------------------------------------------------------------
#  ? GSALight

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data(expression)
expression[1:4,1:3]

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data(sampleInfo)
head(sampleInfo$TN)

## -----------------------------------------------------------------------------
data(targetGenes)
targetGenes[1:3]

## ----error=TRUE---------------------------------------------------------------
data(expression)
data(sampleInfo)
data(targetGenes)
GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes)

## ----error=TRUE---------------------------------------------------------------
expression <- expression[apply(expression,1,sd) != 0,]
GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes)

## -----------------------------------------------------------------------------
GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, 
		   		   	       nperm = 1000, rmGSGenes = 'gene')
head(GSALightResults)

## -----------------------------------------------------------------------------
GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, 
		   		   	       nperm = 1000, method = 'maxmean', restandardize = FALSE, minsize = 10, 
					       maxsize = 30, rmGSGenes = 'gene', verbose = FALSE)

## -----------------------------------------------------------------------------
GSALightResultsMean <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, 
		   		   	       nperm = 1000, method = 'mean', restandardize = FALSE, minsize = 10, 
					       maxsize = 30, rmGSGenes = 'gene', verbose = FALSE)

## -----------------------------------------------------------------------------
GSALightResultsAbs <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, 
		   		   	       nperm = 1000, method = 'absmean', restandardize = FALSE, minsize = 10, 
					       maxsize = 30, rmGSGenes = 'gene', verbose = FALSE)

## -----------------------------------------------------------------------------
head(GSALightResults)
head(GSALightResultsMean)

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head(GSALightResultsAbs)

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GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, 
		   		   	       nperm = NULL, method = 'maxmean', restandardize = FALSE, minsize = 10, 
					       rmGSGenes = 'gene', verbose = FALSE)

## -----------------------------------------------------------------------------
hist(GSALightResults[,'p-value:up-regulated in Control'], main=NULL, xlab='p-value')

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GSALightResultsReStand <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, 
		   		   	       nperm = NULL, method = 'maxmean', restandardize = TRUE, minsize = 10, 
					       rmGSGenes = 'gene', verbose = FALSE)
hist(GSALightResultsReStand[,'p-value:up-regulated in Control'], main=NULL, xlab='p-value')

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GSALightResultsReStand[order(GSALightResultsReStand[,'p-value:up-regulated in Control'],decreasing=F)[1:10], c(2,4)]

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singleGeneAnalysis <- permTestLight(eset = expression, fac = factor(sampleInfo$TN),
		   		  	   	             nperm = 1000,  method = 'mean', verbose = TRUE)
head(singleGeneAnalysis)

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singleWilcox <- wilcoxTest(eset = expression, fac = factor(sampleInfo$TN),
		   		  	   	             tests = "unpaired")
head(singleWilcox)

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fac <- 1:(ncol(expression)/2)
fac <- c(fac, -fac)
head(fac)
tail(fac)

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GSALightResultsPaired <- GSALight(eset = expression, fac = fac, gs = targetGenes, 
		   		   	       nperm = 1000, tests = 'paired', method = 'maxmean', restandardize = TRUE, minsize = 10, 
					       rmGSGenes = 'gene', verbose = FALSE)
head(GSALightResultsPaired)