## ----knitr, echo=FALSE, results="hide"-----------------------------------
knitr::opts_chunk$set(tidy         = FALSE,
                      out.truncate = 80,
                      out.lines    = 6,
                      dev          = 'pdf',
                      include      = TRUE,
                      fig.width    = 6,
                      fig.height   = 6,
                      resolution   = 100,
                      warning      = FALSE,
                      message      = FALSE)


## ----style-Sweave, eval=TRUE, echo=FALSE, results="asis"-----------------
BiocStyle::latex()


## ----loadPKG, echo=FALSE-------------------------------------------------
library(DOSE)
library(clusterProfiler)


## ----options,results='hide',echo=FALSE-----------------------------------
options(digits=3, width=80, prompt=" ", continue=" ")


## ----loading, eval=FALSE, results='hide'---------------------------------
## library(DOSE)
## help(DOSE)


## ----doSim---------------------------------------------------------------
data(DO2EG)
set.seed(123)
a <- sample(names(DO2EG), 10)
a
b <- sample(names(DO2EG), 5)
b
doSim(a[1], b[1], measure="Wang")
doSim(a[1], b[1], measure="Resnik")
doSim(a[1], b[1], measure="Lin")
s <- doSim(a, b, measure="Wang")
s


## ----simplot, fig.cap="Visualizing similarity matrix.", fig.align="center", fig.height=6, fig.width=6, out.width="0.6\\textwidth"----
simplot(s, 
        color.low="white", color.high="red", 
        labs=TRUE, digits=2, labs.size=5, 
        font.size=14, xlab="", ylab="")


## ----geneSim-------------------------------------------------------------
data(EG2DO)
g1 <- sample(names(EG2DO), 5)
g1
g2 <- sample(names(EG2DO), 4)
g2
geneSim(g1[1], g2[1], measure="Wang", combine="BMA")
gs <- geneSim(g1, g2, measure="Wang", combine="BMA")
gs


## ----enrichment analysis-------------------------------------------------
data(geneList)
gene <- names(geneList)[abs(geneList) > 1.5]
head(gene)
x <- enrichDO(gene          = gene,
              ont           = "DO", 
              pvalueCutoff  = 0.05,
              pAdjustMethod = "BH",
              universe      = names(geneList), 
              minGSSize     = 5,
              readable      = FALSE)
head(summary(x))


## ----setReadable---------------------------------------------------------
x <- setReadable(x)
head(summary(x))


## ----barplot, fig.cap="barplot of DO enrichment result.", fig.align="center", fig.height=5, fig.width=6, out.width="0.6\\textwidth"----
barplot(x)


## ----cnetplot, fig.cap="cnetplot of DO enrichment result.", fig.align="center", fig.height=18, fig.width=18----
cnetplot(x, categorySize="pvalue", foldChange=geneList)


## ----clusterProfiler, fig.cap="DOSE with clusterProfiler.", fig.align="center", fig.height=8, fig.width=8, out.width="0.6\\textwidth"----
require(clusterProfiler)
data(gcSample)
cdo <- compareCluster(gcSample, fun="enrichDO")
plot(cdo)


## ----GSEA analysis-------------------------------------------------------
y <- gseAnalyzer(geneList,
                 setType       = "DO",
                 nPerm         = 100, 
                 minGSSize     = 120,
                 pvalueCutoff  = 0.05, 
                 pAdjustMethod = "BH",
                 verbose       = FALSE)
res <- summary(y)
head(res)


## ----gseaplot, fig.cap="gseaplot example.", fig.align="center", fig.height=6, fig.width=8, out.width="0.6\\textwidth"----
topID <- res[1,1]
topID
plot(y, geneSetID = topID)


## ----gseaplot2, eval=FALSE-----------------------------------------------
## plot(y, geneSetID = 1)


## ----enrichmap, fig.cap="enrichMap of DO enrichment result.", fig.align="center", fig.height=10, fig.width=10----
enrichMap(x)


## ----sessInfo, results='asis', echo=FALSE--------------------------------
toLatex(sessionInfo())