###################################################
### chunk number 1: GAPSModSim
###################################################
#line 238 "vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.Rnw"
library('CoGAPS')
data('ModSim')
nIter <- 500000
results <- GAPS(data=ModSim.D, unc=0.01, isPercentError=FALSE,
                numPatterns=3, SAIter=2*nIter, iter = nIter,
                outputDir='ModSimResults')
plotGAPS(results$Amean, results$Pmean, 'ModSimFigs')
message('Deleting analysis results from GAPS for Vignette')
unlink('ModSimResults', recursive=T)


###################################################
### chunk number 2: ModSimPtrue
###################################################
#line 265 "vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.Rnw"
arrayIdx <- 1:ncol(ModSim.P.true)
matplot(arrayIdx, t(ModSim.P.true), type='l', lwd=10)


###################################################
### chunk number 3: SimCoGAPS
###################################################
#line 326 "vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.Rnw"
library('CoGAPS')
data('EasySimGS')
nIter <- 5e+05 
results <- CoGAPS(data=DGS, unc=0.01, isPercentError=FALSE,
                  GStoGenes=gs,
                  numPatterns=3,
                  SAIter = 2*nIter, iter = nIter,
                  outputDir='GSResults', plot=FALSE)
plotGAPS(results$Amean, results$Pmean, 'GSFigs')
message('Deleting analysis results from CoGAPS for Vignette')
unlink('GSResults', recursive=T)


###################################################
### chunk number 4:  eval=FALSE
###################################################
## #line 359 "vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.Rnw"
## library('CoGAPS')
## data('GIST_TS_20084')
## data('TFGSList')
## nIter <- 50000000 
## results <- CoGAPS(data=GIST.D, unc=GIST.S,
##                   GStoGenes=tf2ugFC,
##                   numPatterns=5,
##                   SAIter = 2*nIter, iter = nIter,
##                   outputDir='GISTResults', plot=FALSE)
## plotGAPS(results$Amean, results$Pmean, 'GISTFigs')
## message('Deleting analysis results from CoGAPS for Vignette')
## unlink('GISTResults', recursive=T)