### R code from vignette source 'prostateCancerStockholm.Rnw' ################################################### ### code chunk number 1: prostateCancerStockholm.Rnw:15-16 (eval = FALSE) ################################################### ## library(GEOquery) ################################################### ### code chunk number 2: prostateCancerStockholm.Rnw:22-30 (eval = FALSE) ################################################### ## url <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70769/matrix/" ## destfile <-"GSE70769_series_matrix.txt.gz" ## ## if(!file.exists(destfile)){ ## download.file(paste(url,destfile,sep=""),destfile=destfile) ## } ## ## geoData <- getGEO(filename=destfile) ################################################### ### code chunk number 3: prostateCancerStockholm.Rnw:37-82 (eval = FALSE) ################################################### ## ## pd <- pData(geoData) ## ## ## pd2 <- data.frame("geo_accession" = pd$geo_accession, ## Sample = gsub("tumour tissue_robotic radical prostatetctomy_","",pd$title), ## Gleason=gsub("tumour gleason: ","",pd$characteristics_ch1), ## ECE=gsub("extra capsular extension (ece): ","",pd$characteristics_ch1.2,fixed=TRUE), ## PSM = gsub("positive surgical margins (psm): ","",pd$characteristics_ch1.3,fixed=TRUE), ## BCR = gsub("biochemical relapse (bcr): ","",pd$characteristics_ch1.4,fixed=TRUE), ## Time = gsub("time to bcr (months): ","",pd$characteristics_ch1.5,fixed=TRUE), ## iCluster = gsub("derived data (iclusterplus group): ","",pd$characteristics_ch1.6,fixed=TRUE), ## PSA=gsub("psa at diag: ", "",pd$characteristics_ch1.7,fixed=TRUE), ## ClinicalStage = gsub("clinical stage: ","", pd$characteristics_ch1.8,fixed=TRUE), ## PathStage = gsub("pathology stage: ","",pd$characteristics_ch1.9,fixed=TRUE), ## FollowUpTime = gsub("total follow up (months): ","",pd$characteristics_ch1.10,fixed=TRUE)) ## ## pd2$iCluster <- gsub("NA",NA,pd2$iCluster) ## ## pd2$Gleason <- gsub("N/A", NA, pd2$Gleason) ## pd2$Gleason <- gsub("unknown",NA,pd2$Gleason) ## ## pd2$ECE <- gsub("UNKNOWN",NA,pd2$ECE) ## pd2$ECE[which(pd2$ECE == "")] <- NA ## ## pd2$PSM <- gsub("UNKNOWN",NA,pd2$PSM) ## pd2$PSM[which(pd2$PSM == "")] <- NA ## ## pd2$BCR <- gsub("N/A", NA, pd2$BCR) ## pd2$BCR[which(pd2$BCR == "")] <- NA ## ## pd2$Time <- gsub("N/A", NA, pd2$Time) ## pd2$Time <- gsub("UNKNOWN",NA,pd2$Time) ## pd2$Time[which(pd2$Time == "")] <- NA ## ## pd2$FollowUpTime <- gsub("N/A", NA, pd2$FollowUpTime) ## pd2$FollowUpTime <- gsub("UNKNOWN",NA,pd2$FollowUpTime) ## pd2$FollowUpTime[which(pd2$FollowUpTime == "")] <- NA ## ## ## ## rownames(pd2) <- pd2$geo_accession ## pData(geoData) <- pd2 ## stockholm <- geoData ## save(stockholm, file="data/stockholm.rda",compress="xz")