Organization.

Author: lwaldron

Session5/serenamanara_labexercises/Distance.Rmd

@@ -7,8 +7,8 @@ output: html_document
 
 
 ```{r}
-source("https://bioconductor.org/biocLite.R")
-biocLite()
+#source("https://bioconductor.org/biocLite.R")
+#biocLite()
 library(devtools)
 biocLite("genomicsclass/tissuesGeneExpression")
 library(tissuesGeneExpression)

projects/getTCGAdata.R

@@ -1,7 +1,7 @@
 if( !require(RTCGAToolbox) ){
-  library(devtools)
-  install_github("LiNk-NY/RTCGAToolbox")
-  library(RTCGAToolbox)
+ library(BiocInstaller)
+ biocLite("LiNk-NY/RTCGAToolbox")
+ library(RTCGAToolbox)
 }
 
 all.dates <- getFirehoseRunningDates()
@@ -33,6 +33,20 @@ for (i in 1:length(tcga.res)) {
  eset = try(extract(tcga.res[[i]], "RNAseq2_Gene_Norm"))
  if (is(eset, "try-error"))
  next
- eset = eset[, substr(sampleNames(eset), 14, 15) %in% c("01", "03", "09")]
+ eset = eset[, as.integer(substr(sampleNames(eset), 14, 15)) %in% 1:9]
  saveRDS(eset, file = paste0(names(tcga.res)[i], "_RNAseq2.rds"))
 }
+
+res <- getFirehoseData("SKCM", runDate="20151101", RNAseq2_Gene_Norm=TRUE)
+eset = extract(res, "RNAseq2_Gene_Norm")
+devtools::session_info()
+
+expdat <- res@RNASeq2GeneNorm
+colnames(expdat) <- tolower(substr(colnames(expdat), 1, 12))
+clindat <- res@Clinical
+rownames(clindat) <- gsub(".", "-", rownames(clindat), fixed=TRUE)
+clindat <- clindat[rownames(clindat) %in% colnames(expdat), ]
+expdat <- expdat[, match(rownames(clindat), colnames(expdat))]
+
+all.equal(colnames(expdat), rownames(clindat))
+eset <- ExpressionSet(assayData=expdat, phenoData=AnnotatedDataFrame(clindat))