mdgsa_vignette.R
In mdgsa: Multi Dimensional Gene Set Analysis.

## ----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)

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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)

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plot (fit$p.value[,"BCR - NEG"], rindex)

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anmat[1:3,]
annot <- annotMat2list (anmat)
length (annot)

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lapply (annot[1:3], head, n= 3)

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annot <- annotFilter (annot, rindex)

## ----uvGsa--------------------------------------------------------------------
res.uv <- uvGsa (rindex, annot)

## -----------------------------------------------------------------------------
res.uv[1:3,]

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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)

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res.md[1:3,]

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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"])

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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())