## ----eval=FALSE--------------------------------------------------------------- # library("GEOquery") # gse <- getGEO(filename="GSE56761_series_matrix.txt") # pdata <- pData(gse)[,grepl("characteristics",names(pData(gse)))] ## ----eval=FALSE--------------------------------------------------------------- # names(pdata) <- c("strain","treatment","time","replicate") # pdataclean <- data.frame(strain=ifelse(grepl("wild type",pdata$strain),"wt","mut"), # minute=sub("time \\(min\\): (.*)","\\1",pdata$time), # replicate=paste0("r",sub("replicate: (.*)","\\1",pdata$replicate)), # row.names=rownames(pdata)) # pdataclean$id <- paste(pdataclean$strain,pdataclean$minute,pdataclean$replicate,sep="_") # pdataclean$strain <- relevel(pdataclean$strain, "wt") # pdataclean$minute <- factor(pdataclean$minute, levels=c("0","15","30","60","120","180")) ## ----eval=FALSE--------------------------------------------------------------- # load("GSE56761_count_data.Rdata") # stopifnot(all.equal(rownames(reads.GSE56761), as.character(gene.annotations$pombase_id))) # colnames(reads.GSE56761) <- tolower(colnames(reads.GSE56761)) # stopifnot(all.equal(colnames(reads.GSE56761), pdataclean$id)) # colnames(reads.GSE56761) <- rownames(pdataclean) # library("SummarizedExperiment") # coldata <- DataFrame(pdataclean) ## ----eval=FALSE--------------------------------------------------------------- # genes <- gene.annotations # rowranges <- GRanges(seqnames=genes$chromosome, # ranges=IRanges(genes$start, # genes$end), # strand=genes$strand, # genes[,6:7]) # mcols(rowranges)$symbol <- as.character(mcols(rowranges)$symbol) # names(rowranges) <- genes$pombase_id ## ----eval=FALSE--------------------------------------------------------------- # library("annotate") # metadata <- pmid2MIAME("24853205") # metadata@url <- "http://www.ncbi.nlm.nih.gov/pubmed/24853205" ## ----eval=FALSE--------------------------------------------------------------- # fission <- SummarizedExperiment(SimpleList(counts=reads.GSE56761), # rowRanges=rowranges, # colData=coldata, # metadata=list(metadata)) # save(fission, file="fission.RData")