## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ---- include = FALSE--------------------------------------------------------- library (knitr) ## this is needed when R CMD build opts_chunk$set (message = FALSE) ## ----------------------------------------------------------------------------- library (ALL) data (ALL) des.mat <- model.matrix (~ 0 + mol.biol, data = ALL) colnames (des.mat) <- c("ALL", "BCR", "E2A", "NEG", "NUP", "p15") head (des.mat) ## ----------------------------------------------------------------------------- library (limma) cont.mat <- makeContrasts (ALL-NEG, BCR-NEG, levels = des.mat) cont.mat fit <- lmFit (ALL, design = des.mat) fit <- contrasts.fit (fit, cont.mat) fit <- eBayes (fit) ## ----------------------------------------------------------------------------- fit$t[1:3,] fit$p.value[1:3,] ## ----------------------------------------------------------------------------- library (hgu95av2.db) anmat <- toTable (hgu95av2PATH) anmat[1:3,] ## ----------------------------------------------------------------------------- fit$t[1:3, "BCR - NEG"] fit$p.value[1:3, "BCR - NEG"] ## ----------------------------------------------------------------------------- library (mdgsa) ## ----------------------------------------------------------------------------- rindex <- pval2index (pval = fit$p.value[,"BCR - NEG"], sign = fit$t[,"BCR - NEG"]) rindex <- indexTransform (rindex) rindex[1:3] ## ----------------------------------------------------------------------------- plot (fit$t[,"BCR - NEG"], rindex) ## ----------------------------------------------------------------------------- plot (fit$p.value[,"BCR - NEG"], rindex) ## ----------------------------------------------------------------------------- anmat[1:3,] annot <- annotMat2list (anmat) length (annot) ## ----------------------------------------------------------------------------- lapply (annot[1:3], head, n= 3) ## ----------------------------------------------------------------------------- annot <- annotFilter (annot, rindex) ## ----uvGsa-------------------------------------------------------------------- res.uv <- uvGsa (rindex, annot) ## ----------------------------------------------------------------------------- res.uv[1:3,] ## ----------------------------------------------------------------------------- res.uv[,"pat"] <- uvPat (res.uv, cutoff = 0.05) table (res.uv[,"pat"]) ## ---- results = "hide"-------------------------------------------------------- res.uv[,"KEGG"] <- getKEGGnames (res.uv) ## ----------------------------------------------------------------------------- res <- uvSignif (res.uv) res[,c("pat", "KEGG")] ## ----------------------------------------------------------------------------- fit$t[1:3,] fit$p.value[1:3,] ## ----------------------------------------------------------------------------- rindex <- pval2index (pval = fit$p.value, sign = fit$t) rindex <- indexTransform (rindex) rindex[1:3,] ## ----------------------------------------------------------------------------- plot (rindex, pch = ".") ## ----mdGsa-------------------------------------------------------------------- res.md <- mdGsa (rindex, annot) ## ----------------------------------------------------------------------------- res.md[1:3,] ## ----------------------------------------------------------------------------- res.md[,"pat"] <- mdPat (res.md) table (res.md[,"pat"]) ## ---- results = "hide"-------------------------------------------------------- res.md[,"KEGG"] <- getKEGGnames (res.md) res.md[1:3,] ## ----------------------------------------------------------------------------- Q3 <- rownames (res.md)[res.md$pat == "q3f"] Q3 plotMdGsa (rindex, block = annot[[Q3]], main = res.md[Q3, "KEGG"]) ## ----------------------------------------------------------------------------- BI <- rownames (res.md)[res.md$pat == "b13"] plotMdGsa (rindex, block = annot[[BI]], main = res.md[BI, "KEGG"]) ## ----------------------------------------------------------------------------- rownames (res.md)[res.md$pat == "yl"] YL <- "00280" plotMdGsa (rindex, block = annot[[YL]], main = res.md[YL, "KEGG"]) ## ----------------------------------------------------------------------------- Q2 <- rownames (res.md)[res.md$pat == "q2f"] Q2 plotMdGsa (rindex, block = annot[[Q2]], main = res.md[Q2, "KEGG"]) ## ----------------------------------------------------------------------------- rownames (res.md)[res.md$pat == "yh"] YH <- "05332" plotMdGsa (rindex, block = annot[[YH]], main = res.md[YH, "KEGG"]) ## ----------------------------------------------------------------------------- sessionInfo() ## ---- echo = FALSE, results = "asis"------------------------------------------ toLatex (sessionInfo())