## ----style, echo=FALSE, results="asis", message=FALSE--------------------
BiocStyle::markdown()
knitr::opts_chunk$set(tidy = FALSE,
                      warning = FALSE,
                      message = FALSE)

## ----echo=FALSE, results='hide', message=FALSE---------------------------
library(DOSE)
library(clusterProfiler)

## ----eval=FALSE----------------------------------------------------------
## library(DOSE)
## help(DOSE)

## ------------------------------------------------------------------------
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(s, 
        color.low="white", color.high="red", 
        labs=TRUE, digits=2, labs.size=5, 
        font.size=14, xlab="", ylab="")

## ----warning=FALSE-------------------------------------------------------
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

## ------------------------------------------------------------------------
clusterSim(g1, g2, measure="Wang", combine="BMA")

## ------------------------------------------------------------------------
clusters <- list(a=g1, b=g2, c=sample(names(EG2DO), 6))
mclusterSim(clusters, measure="Wang", combine="BMA")

## ------------------------------------------------------------------------
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,
              qvalueCutoff  = 0.05,
              readable      = FALSE)
head(summary(x))

## ------------------------------------------------------------------------
x <- setReadable(x, 'org.Hs.eg.db')
head(summary(x))

## ------------------------------------------------------------------------
barplot(x)

## ------------------------------------------------------------------------
dotplot(x)

## ----fig.width=18, fig.height=18-----------------------------------------
cnetplot(x, categorySize="pvalue", foldChange=geneList)

## ------------------------------------------------------------------------
require(clusterProfiler)
data(gcSample)
cdo <- compareCluster(gcSample, fun="enrichDO")
plot(cdo)

## ------------------------------------------------------------------------
y <- gseDO(geneList,
           nPerm         = 100, 
                 minGSSize     = 120,
                 pvalueCutoff  = 0.2, 
                 pAdjustMethod = "BH",
                 verbose       = FALSE)
res <- summary(y)
head(res)

## ----fig.height=6, fig.width=8-------------------------------------------
topID <- res[1,1]
topID
plot(y, geneSetID = topID)

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

## ----fig.height=10, fig.width=10-----------------------------------------
enrichMap(x)

## ----echo=FALSE----------------------------------------------------------
sessionInfo()