## ----eval=FALSE----------------------------------------------------------
#  source("http://bioconductor.org/biocLite.R")
#  biocLite("RTCGAToolbox")

## ------------------------------------------------------------------------
library(RTCGAToolbox)

# Valid aliases
getFirehoseDatasets()

## ------------------------------------------------------------------------
# Valid stddata runs
stddata <- getFirehoseRunningDates()
stddata

## ------------------------------------------------------------------------
# Valid analysis running dates (will return 3 recent date)
gisticDate <- getFirehoseAnalyzeDates(last=3)
gisticDate

## ----eval=TRUE,message=FALSE---------------------------------------------
# READ mutation data and clinical data
brcaData <- getFirehoseData(dataset="READ", runDate="20150402",
    forceDownload=TRUE, clinical=TRUE, Mutation=TRUE)

## ------------------------------------------------------------------------
data(RTCGASample)
RTCGASample

## ------------------------------------------------------------------------
# Differential gene expression analysis for gene level RNA data.
diffGeneExprs <- getDiffExpressedGenes(dataObject=RTCGASample, DrawPlots=TRUE,
    adj.method="BH", adj.pval=0.05, raw.pval=0.05, logFC=2, hmTopUpN=10,
    hmTopDownN=10)
# Show head for expression outputs
diffGeneExprs
showResults(diffGeneExprs[[1]])
toptableOut <- showResults(diffGeneExprs[[1]])

## ------------------------------------------------------------------------
#Correlation between gene expression values and copy number
corrGECN <- getCNGECorrelation(dataObject=RTCGASample, adj.method="BH",
    adj.pval=0.9, raw.pval=0.05)
corrGECN
showResults(corrGECN[[1]])
corRes <- showResults(corrGECN[[1]])

## ------------------------------------------------------------------------
# Mutation frequencies
mutFrq <- getMutationRate(dataObject=RTCGASample)
head(mutFrq[order(mutFrq[, 2], decreasing=TRUE), ])

## ----fig.width=6,fig.height=6,fig.align='center'-------------------------
# Creating survival data frame and running analysis for
# FCGBP which is one of the most frequently mutated gene in the toy data
# Running following code will provide following KM plot.
clinicData <- getData(RTCGASample,"clinical")
head(clinicData)
clinicData <- clinicData[, 3:5]
clinicData[is.na(clinicData[, 3]), 3] <- clinicData[is.na(clinicData[, 3]), 2]
survData <- data.frame(Samples=rownames(clinicData),
    Time=as.numeric(clinicData[, 3]), Censor=as.numeric(clinicData[, 1]))
getSurvival(dataObject=RTCGASample, geneSymbols=c("FCGBP"), sampleTimeCensor=survData)

## ------------------------------------------------------------------------
# Note: This function is provided for real dataset test since the toy dataset is small.
RTCGASample

## ----message=FALSE-------------------------------------------------------
RTCGASampleClinical <- getData(RTCGASample, "clinical")
RTCGASampleRNAseqCounts <- getData(RTCGASample, "RNASeqGene")
RTCGASampleCN <- getData(RTCGASample, "GISTIC", "AllByGene")

## ----eval=FALSE----------------------------------------------------------
#  # BRCA data with mRNA (Both array and RNASeq), GISTIC processed copy number data
#  # mutation data and clinical data
#  # (Depends on bandwidth this process may take long time)
#  brcaData <- getFirehoseData (dataset="BRCA", runDate="20140416",
#      gistic2Date="20140115", clinic=TRUE, RNAseqGene=TRUE, mRNAArray=TRUE,
#      Mutation=TRUE)
#  
#  # Differential gene expression analysis for gene level RNA data.
#  # Heatmaps are given below.
#  diffGeneExprs <- getDiffExpressedGenes(dataObject=brcaData,DrawPlots=TRUE,
#      adj.method="BH", adj.pval=0.05, raw.pval=0.05, logFC=2, hmTopUpN=100,
#      hmTopDownN=100)
#  # Show head for expression outputs
#  diffGeneExprs
#  showResults(diffGeneExprs[[1]])
#  toptableOut <- showResults(diffGeneExprs[[1]])
#  
#  # Correlation between expresiion profiles and copy number data
#  corrGECN <- getCNGECorrelation(dataObject=brcaData, adj.method="BH",
#      adj.pval=0.05, raw.pval=0.05)
#  
#  corrGECN
#  showResults(corrGECN[[1]])
#  corRes <- showResults(corrGECN[[1]])
#  
#  # Gene mutation frequincies in BRCA dataset
#  mutFrq <- getMutationRate(dataObject=brcaData)
#  head(mutFrq[order(mutFrq[,2],decreasing=TRUE),])
#  
#  # PIK3CA which is one of the most frequently mutated gene in BRCA dataset
#  # KM plot is given below.
#  clinicData <- getData(brcaData,"clinical")
#  head(clinicData)
#  clinicData <- clinicData[, 3:5]
#  clinicData[is.na(clinicData[, 3]), 3] <- clinicData[is.na(clinicData[, 3]), 2]
#  survData <- data.frame(Samples=rownames(clinicData),
#      Time=as.numeric(clinicData[, 3]), Censor=as.numeric(clinicData[, 1]))
#  getSurvival(dataObject=brcaData, geneSymbols=c("PIK3CA"),
#      sampleTimeCensor=survData)

## ----eval=FALSE----------------------------------------------------------
#  # Creating dataset analysis summary figure with getReport.
#  # Figure will be saved as PDF file.
#  library("Homo.sapiens")
#  locations <- genes(Homo.sapiens, columns="SYMBOL")
#  locations <- as.data.frame(locations)
#  locations <- locations[,c(6,1,5,2:3)]
#  locations <- locations[!is.na(locations[,1]), ]
#  locations <- locations[!duplicated(locations[,1]), ]
#  rownames(locations) <- locations[,1]
#  getReport(dataObject=brcaData, DGEResult1=diffGeneExprs[[1]],
#      DGEResult2=diffGeneExprs[[2]], geneLocations=locations)

## ------------------------------------------------------------------------
data(RTCGASample)

## ------------------------------------------------------------------------
sessionInfo()

