## ---- eval=TRUE, warnings = FALSE, echo=TRUE,message=FALSE---------------

library(ChIPanalyser)

#Load data
data(ChIPanalyserData)


# Loading DNASequenceSet from BSgenome object
# We recommend using the latest version of the genome 
# Please ensure that all your data is aligned to the same version of the genome

library(BSgenome.Dmelanogaster.UCSC.dm3)

DNASequenceSet <-getSeq(BSgenome.Dmelanogaster.UCSC.dm3)



#Loading Position Frequency Matrix

PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")

#Checking if correctly loaded
ls()


## ----eval=TRUE, warnings = FALSE-----------------------------------------
eveLocusChip<-processingChIP(profile=eveLocusChip,
                              loci=eveLocus,
                              cores=1)
eveLocusChip

## ---- eval =TRUE---------------------------------------------------------
# PFMs are automatically converted to PWM when build genomicProfiles
GP<-genomicProfiles(PFM=PFM,PFMFormat="raw")
GP

## ---- eval=FALSE---------------------------------------------------------
#  GP<-genomicProfiles(PWM=PositionWeightMatrix)

## ----eval=TRUE,warnings=FALSE--------------------------------------------
## surpress dependency warnings
optimal<-suppressWarnings(computeOptimal(genomicProfiles=GP,
                        DNASequenceSet=DNASequenceSet,
                        ChIPScore=eveLocusChip,
                        chromatinState=Access))

## ---- eval=TRUE, echo=TRUE-----------------------------------------------
 ## Lambda Values
 seq(0.25,5,by=0.25)

 ## Bound Molecule Values
 c(1, 10, 20, 50, 100,
    200, 500,1000,2000, 5000,10000,20000,50000, 100000,
    200000, 500000, 1000000)

## ---- eval =T------------------------------------------------------------
optimalParam<-optimal$Optimal
optimalParam$OptimalParameters

## ---- eval=TRUE, warnings = FALSE, fig.width=10, fig.height=8------------
# Plotting Optimal heat maps
par(oma=c(0,0,3,0))
layout(matrix(1:8,ncol=4, byrow=T),width=c(6,1.5,6,1.5),height=c(1,1))
plotOptimalHeatMaps(optimalParam,layout=FALSE)


## ----eval=TRUE-----------------------------------------------------------
optimalParam<-searchSites(optimal,lambdaPWM=1.25,BoundMolecules=10000)

## ---- eval=TRUE,fig.width=12, fig.height=4.5-----------------------------
plotOccupancyProfile(predictedProfile=optimalParam$ChIPProfiles,
                     ChIPScore=eveLocusChip,
                     chromatinState=Access,
                     occupancy=optimalParam$Occupancy,
                     goodnessOfFit=optimalParam$goodnessOfFit)

## ---- eval =TRUE---------------------------------------------------------
## Suggested Parameters to start with.
parameterOptions()

## Changing parameters
PO <- parameterOptions(noiseFilter="sigmoid",chipSd=150,chipMean=150,lociWidth=30000)

## ----eval=FALSE----------------------------------------------------------
#  ## Top 50 loci based on ChIP score
#  processingChIP(profile="/path/to/ChIP",
#                 loci=NULL,
#                 reduce=50,
#                 parameterOptions=PO)
#  
#  ## Top 50 loci ALSO containing peaks
#  processingChIP(profile="/path/to/ChIP",
#                 loci=NULL,
#                 reduce=50,
#                 peaks="/path/to/peaks",
#                 parameterOptions=PO)
#  
#  ## Top 50 loci containing BOTH peaks and Accessible DNA
#  processingChIP(profile="/path/to/ChIP",
#                 loci=NULL,
#                 reduce=50,
#                 peaks="/path/to/peaks",
#                 chromatinState="/path/to/chromatinState"
#                 parameterOptions=PO)
#  

## ---- eval=TRUE----------------------------------------------------------
str(genomicProfiles())

GP <- genomicProfiles(PFM=PFM, PFMFormat="raw", BPFrequency=DNASequenceSet)
GP

## ---- eval=FALSE---------------------------------------------------------
#  ## Parsing pre computed parameters (processingChIP function)
#  GP<-genomicProfiles(PFM=PFM, PFMFormat="raw", BPFrequency=DNASequenceSet,
#                      ChIPScore=ChIPScore)
#  
#  ## Parsing pre assigned function (parameterOptions)
#  parameterOptions<-parameterOptions(lambdaPWM=c(1,2,3),
#                                     boundMolecules=c(5,50,500))
#  GP<-genomicProfiles(PFM=PFM, PFMFormat="raw", BPFrequency=DNASequenceSet,
#                      parameterOptions=parameterOptions)
#  
#  ## Direct parameter assignement
#  
#  GP<-genomicProfiles(PFM=PFM, PFMFormat="raw", BPFrequency=DNASequenceSet,
#                      lambdaPWM=c(1,2,3),boundMolecules=c(4,500,8000))

## ---- eval=FALSE---------------------------------------------------------
#  ## Setting custom parameters
#  OP<-parameterOptions(lambdaPWM=seq(1,10,by=0.5),
#                       boundMolecules=seq(1,100000, length.out=20))
#  
#  ## Computing ONLY Optimal Parameters and MSE as goodness Of Fit metric
#  optimal<-computeOptimal(genomicProfiles=GP,
#                          DNASequenceSet=DNASequenceSet,
#                          ChIPScore=eveLocusChip,
#                          chromatinState=Access,
#                          parameterOptions=OP,
#                          optimalMethod="MSE",
#                          returnAll=FALSE)
#  
#  ### Computing ONLY Optimal Parameters and using Rank slection method
#  optimal<-computeOptimal(genomicProfiles=GP,
#                          DNASequenceSet=DNASequenceSet,
#                          ChIPScore=eveLocusChip,
#                          chromatinState=Access,
#                          parameterOptions=OP,
#                          optimalMethod="all",
#                          rank=TRUE)
#  

## ---- eval=FALSE---------------------------------------------------------
#  ## Extracted Optimal Parameters
#  optimalParam<-optimal$Optimal
#  
#  ## Plotting heat maps
#  plotOptimalHeatMaps(optimalParam,overlay=TRUE)

## ----eval=TRUE,warnings=FALSE--------------------------------------------

## Creating genomic Profiles object with PFMs and associated parameters
GP <- genomicProfiles(PFM=PFM,PFMFormat="raw",BPFrequency=DNASequenceSet,
                      lambdaPWM=1, boundMolecules=58794)

## Computing Genome Wide Score required
GW <- computeGenomeWideScores(genomicProfiles=GP,
                              DNASequenceSet=DNASequenceSet,
                              chromatinState=Access)
GW
## Computing PWM score above threshold
pwm <- computePWMScore(genomicProfiles=GW,
                       DNASequenceSet=DNASequenceSet,
                       loci=eveLocusChip,
                       chromatinState=Access)
pwm
## Computing Occupancy of sites above threshold

occup <- computeOccupancy(genomicProfiles=pwm)
occup
## Compute ChIP seq like profiles

chip <- computeChIPProfile(genomicProfiles=occup,
                            loci=eveLocusChip)
chip
## Compute goodness Of Fit of model
accu <- profileAccuracyEstimate(genomicProfiles=chip,
                                ChIPScore=eveLocusChip)
accu


## ---- eval=TRUE,fig.width=12, fig.height=4.5-----------------------------

plotOccupancyProfile(predictedProfile=chip,
                     ChIPScore=eveLocusChip,
                     chromatinState=Access,
                     occupancy=occup,
                     goodnessOfFit=accu,
                     geneRef=geneRef)

## ---- eval=TRUE,echo=TRUE------------------------------------------------
parameterOptions()

## ---- eval=T, echo=T-----------------------------------------------------
str(genomicProfiles())

## ---- eval=F, echo=T-----------------------------------------------------
#      ## Accessors and Setters for parameterOptions and genomicProfiles
#      avrageExpPWMScore(obj)
#      backgroundSignal(obj)
#      backgroundSignal(obj)<-value
#      boundMolecules(obj)
#      boundMolecules(obj)<-value
#      BPFrequency(obj)
#      BPFrequency(obj)<-value
#      chipMean(obj)
#      chipMean(obj)<-value
#      chipSd(obj)
#      chipSd(obj)<-value
#      chipSmooth(obj)
#      chipSmooth(obj)<-value
#      DNASequenceLength(obj)
#      drop(obj)
#      lambdaPWM(obj)
#      lambdaPWM(obj)<-value
#      lociWidth(obj)
#      lociWidth(obj)<-value
#      maxPWMScore(obj)
#      maxSignal(obj)
#      maxSignal(obj)<-value
#      minPWMScore(obj)
#      naturalLog(obj)
#      naturalLog(obj)<-value
#      noiseFilter(obj)
#      noiseFilter(obj)<-value
#      noOfSites(obj)
#      noOfSites(obj)<-value
#      PFMFormat(obj)
#      PFMFormat(obj)<-value
#      ploidy(obj)
#      ploidy(obj)<-value
#      PositionFrequencyMatrix(obj)
#      PositionFrequencyMatrix(obj)<-value
#      PositionWeightMatrix(obj)
#      PositionWeightMatrix<-value
#      profiles(obj)
#      PWMpseudocount(obj)
#      PWMpseudocount(obj)<-value
#      PWMThreshold(obj)
#      PWMThreshold(obj)<-value
#      removeBackground(obj)
#      removeBackground(obj)<-value
#  
#      stepSize(obj)
#      stepSize(obj)<-value
#      strandRule(obj)
#      strandRule(obj)<-value
#      whichstrand(obj)
#      whichstrand(obj)<-value
#  
#      ## ChIPScore slots accessors
#      loci(obj)
#      scores(obj)

## ----eval=T--------------------------------------------------------------
sessionInfo()

