## ---- echo = FALSE, results = "asis"------------------------------------------ BiocStyle::markdown() options(bitmapType = "cairo") ## ---- eval = FALSE------------------------------------------------------------ # # library(knitr) # purl(system.file("doc/RefactoredAffycoretools.Rmd", package="affycoretools")) # # ## ----start-------------------------------------------------------------------- suppressMessages(library(affycoretools)) data(sample.ExpressionSet) eset <- sample.ExpressionSet eset ## ---- include = FALSE--------------------------------------------------------- featureNames(eset) <- gsub("/", "_", featureNames(eset)) ## ----model-------------------------------------------------------------------- suppressMessages(library(hgu95av2.db)) eset <- annotateEset(eset, hgu95av2.db) suppressMessages(library(limma)) pd <- pData(phenoData(eset)) design <- model.matrix(~0+type+sex, pd) colnames(design) <- gsub("type|sex", "", colnames(design)) contrast <- matrix(c(1,-1,0)) colnames(contrast) <- "Case vs control" fit <- lmFit(eset, design) fit2 <- contrasts.fit(fit, contrast) fit2 <- eBayes(fit) topTable(fit2, 1)[,1:4] ## ----output------------------------------------------------------------------- suppressMessages(library(ReportingTools)) htab <- HTMLReport("afile", "My cool results") publish(topTable(fit2, 1), htab) finish(htab) ## ----rtools------------------------------------------------------------------- htab <- HTMLReport("afile2", "My cool results, ReportingTools style") publish(fit2, htab, eset, factor = pd$type, coef = 1, n = 10) finish(htab) ## ----output2------------------------------------------------------------------ d.f <- topTable(fit2, 2) out <- makeImages(df = d.f, eset = eset, grp.factor = pd$type, design = design, contrast = contrast, colind = 1, repdir = ".") htab <- HTMLReport("afile3", "My cool results, affycoretools style") publish(out$df, htab, .mofifyDF = list(entrezLinks, affyLinks)) finish(htab) ## ----param2------------------------------------------------------------------- grps <- factor(apply(pd[,1:2], 1, paste, collapse = "_")) design <- model.matrix(~0+grps) colnames(design) <- gsub("grps", "", colnames(design)) contrast <- matrix(c(1,-1,0,0, 0,0,1,-1, 1,-1,-1,1), ncol = 3) colnames(contrast) <- c("Female_Case vs Female_Control", "Male_Case vs Male_Control", "Interaction") fit <- lmFit(eset, design) fit2 <- contrasts.fit(fit, contrast) fit2 <- eBayes(fit2) ## ----output3------------------------------------------------------------------ ## get a list containing the output for each comparison out <- lapply(1:3, function(x) topTable(fit2, x)) ## process the output to add images htab <- lapply(1:3, function(x){ tmp <- HTMLReport(gsub("_", " ", colnames(contrast)[x]), colnames(contrast)[x], "./reports") tmp2 <- makeImages(out[[x]], eset, grps, design, contrast, x) publish(tmp2$df, tmp, .modifyDF = list(affyLinks, entrezLinks)) finish(tmp) return(tmp) }) ## ----table, results = "asis"-------------------------------------------------- d.f <- data.frame(Comparison = sapply(htab, function(x) XML::saveXML(Link(x))), "Number significant" = sapply(out, nrow), check.names = FALSE) kable(d.f, caption = "Number of significant genes.", format = "html", row.names = FALSE) ## ----makevenn, results = "asis"----------------------------------------------- collist <- list(1:2) venn <- makeVenn(fit2, contrast, design, collist = collist, adj.meth = "none") ## generate a list of captions for each Venn. ## we only have one, so it's a list of length 1. ## we are using the BiocStyle package to control formatting, ## so the first sentence will be bolded and in blue. cap <- list(paste("A Venn diagram. Note that the first sentence is bolded", "and blue, whereas the rest is normal type and black. Usually", "one would use a more useful caption than this one.")) vennInLine(venn, cap) ## ---- echo = FALSE------------------------------------------------------------ sessionInfo()