## ----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")