### R code from vignette source 'prostateCancerTaylor.Rnw' ################################################### ### code chunk number 1: prostateCancerTaylor.Rnw:21-23 (eval = FALSE) ################################################### ## library(GEOquery) ## library(org.Hs.eg.db) ################################################### ### code chunk number 2: prostateCancerTaylor.Rnw:29-38 (eval = FALSE) ################################################### ## ## url <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE21nnn/GSE21034/matrix/" ## destfile <-"GSE21034-GPL10264_series_matrix.txt.gz" ## ## if(!file.exists(destfile)){ ## download.file(paste(url,destfile,sep=""),destfile=destfile) ## } ## ## geoData <- getGEO(filename=destfile) ################################################### ### code chunk number 3: prostateCancerTaylor.Rnw:44-53 (eval = FALSE) ################################################### ## library(org.Hs.eg.db) ## entrezid <- unlist(mget(as.character(fData(geoData)[,2]), ## revmap(org.Hs.egREFSEQ),ifnotfound = NA)) ## ## anno <- data.frame(fData(geoData), Entrez = entrezid) ## anno <- anno[!is.na(anno$Entrez),] ## fData(geoData) <- data.frame(anno, ## Gene=unlist(mget(as.character(anno$Entrez), ## org.Hs.egSYMBOL,ifnotfound=NA))) ################################################### ### code chunk number 4: prostateCancerTaylor.Rnw:58-68 (eval = FALSE) ################################################### ## pd <- pData(geoData) ## ## pd2 <- data.frame("geo_accession" = pd$geo_accession, ## Sample = gsub("sample id: ", "", pd$characteristics_ch1), ## Sample_Group = gsub("disease status: ","", pd$characteristics_ch1.2), ## Gleason=gsub("biopsy_gleason_grade: ", "", pd$characteristics_ch1.4), ## Stage = gsub("clint_stage: ", "", pd$characteristics_ch1.5), ## Path_Stage = gsub("pathological_stage: ","",pd$characteristics_ch1.6)) ## ## rownames(pd2) <- pd2$geo_accession ################################################### ### code chunk number 5: prostateCancerTaylor.Rnw:73-86 (eval = FALSE) ################################################### ## fpath <- system.file("extdata", "STable1.csv",package="prostateCancerTaylor") ## extraClin <- read.csv(fpath) ## ## pd2 <- merge(pd2, extraClin, by.x=2,by.y=1,all.x=TRUE,sort=FALSE) ## pd2$Time <- pd2$BCR_FreeTime ## pd2$Event <- pd2$BCR_Event == "BCR_Algorithm" ## pd2$Gleason <- paste(pd2$PathGG1,pd2$PathGG2,sep="+") ## pd2$Gleason[is.na(pd2$PathGG1) | is.na(pd2$PathGG2)] <- NA ## pData(geoData) <- pd2[,c("Sample","geo_accession", ## "Sample_Group","Gleason","Stage","Path_Stage", ## "Type","Copy.number.Cluster","Time","Event")] ## taylor <- geoData ## save(taylor, file="data/taylor.rda",compress = "xz")