## ---- eval=FALSE---------------------------------------------------------
#  library(BiocInstaller)
#  biocLite("LiNk-NY/RTCGAToolbox")

## ---- message=FALSE------------------------------------------------------
library(RTCGAToolbox)
(rundates <- getFirehoseRunningDates())

## ------------------------------------------------------------------------
(analysisdates <- getFirehoseAnalyzeDates())

## ---- eval=FALSE---------------------------------------------------------
#  ov <- getFirehoseData("OV", runDate=rundates[1], gistic2_Date=analysisdates[1], RNAseq_Gene=TRUE,
#          miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP=TRUE, CNV_SNP=TRUE, CNA_Seq=TRUE,
#          CNA_CGH=TRUE,  Methylation=TRUE, Mutation=TRUE, mRNA_Array=TRUE, miRNA_Array=TRUE,
#          RPPA=TRUE, todir = NULL)
#  
#  gbm <- getFirehoseData("GBM", runDate=rundates[1], gistic2_Date=analysisdates[1], RNAseq_Gene=TRUE,
#         	miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP=TRUE, CNV_SNP=TRUE, CNA_Seq=TRUE,
#          CNA_CGH=TRUE,  Methylation=TRUE, Mutation=TRUE, mRNA_Array=TRUE, miRNA_Array = TRUE,
#          RPPA=TRUE, todir = NULL)
#  
#  coad <- getFirehoseData("COAD", runDate=rundates[1], gistic2_Date=analysisdates[1], RNAseq_Gene=TRUE,
#          miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP = TRUE, CNV_SNP=TRUE, CNA_Seq = TRUE,
#          CNA_CGH = TRUE, Methylation = TRUE, Mutation = TRUE, mRNA_Array = TRUE, miRNA_Array = TRUE,
#          RPPA = TRUE, todir = NULL)
#  
#  laml <- getFirehoseData("LAML", runDate=rundates[1], gistic2_Date=analysisdates[1], RNAseq_Gene=TRUE,
#            miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP = TRUE, CNV_SNP=TRUE, CNA_Seq = TRUE,
#            CNA_CGH = TRUE, Methylation = TRUE, Mutation = TRUE, mRNA_Array = TRUE, miRNA_Array = TRUE,
#            RPPA = TRUE, todir = NULL)
#  
#  blca <- getFirehoseData("BLCA", runDate=rundates[1], gistic2_Date=analysisdates[1], RNAseq_Gene=TRUE,
#            miRNASeq_Gene=TRUE, RNAseq2_Gene_Norm=TRUE, CNA_SNP = TRUE, CNV_SNP=TRUE, CNA_Seq = TRUE,
#            CNA_CGH = TRUE, Methylation = TRUE, Mutation = TRUE, mRNA_Array = TRUE, miRNA_Array = TRUE,
#            RPPA = TRUE, todir = NULL)

## ------------------------------------------------------------------------
library(bioc2015multiomicsworkshop)
data(laml)
laml

## ------------------------------------------------------------------------
choices <- tolower(gsub("_", "", c("RNAseq_Gene", "miRNASeq_Gene",
             "RNAseq2_Gene_Norm", "CNA_SNP", "CNV_SNP", "CNA_Seq",
             "CNA_CGH", "Methylation", "Mutation", "mRNA_Array",
             "miRNA_Array", "RPPA")))

## ------------------------------------------------------------------------
cna <- extract(laml, "cnasnp", clinical=TRUE)
cna

## ------------------------------------------------------------------------
rnaseq <- extract(laml, "rnaseqgene", clinical=TRUE)
rnaseq

## ------------------------------------------------------------------------
summary(names(cna) %in% sampleNames(rnaseq))

## ------------------------------------------------------------------------
elementMetadata(cna)[1:2, 1:4]
pData(rnaseq)[1:2, 1:4]