## ----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,
                      message      = FALSE,
                      warning      = FALSE)


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


## ----loadPKG, echo=FALSE-------------------------------------------------
library(DOSE)
library(GO.db)
library(org.Hs.eg.db)
library(clusterProfiler)


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


## ----bitr----------------------------------------------------------------
x <- c("GPX3",  "GLRX",   "LBP",   "CRYAB", "DEFB1", "HCLS1",   "SOD2",   "HSPA2", 
       "ORM1",  "IGFBP1", "PTHLH", "GPC3",  "IGFBP3","TOB1",    "MITF",   "NDRG1", 
       "NR1H4", "FGFR3",  "PVR",   "IL6",   "PTPRM", "ERBB2",   "NID2",   "LAMB1", 
       "COMP",  "PLS3",   "MCAM",  "SPP1",  "LAMC1", "COL4A2",  "COL4A1", "MYOC",  
       "ANXA4", "TFPI2",  "CST6",  "SLPI",  "TIMP2", "CPM",     "GGT1",   "NNMT",
       "MAL",   "EEF1A2", "HGD",   "TCN2",  "CDA",   "PCCA",    "CRYM",   "PDXK",  
       "STC1",  "WARS",  "HMOX1", "FXYD2", "RBP4",   "SLC6A12", "KDELR3", "ITM2B")
eg = bitr(x, fromType="SYMBOL", toType="ENTREZID", annoDb="org.Hs.eg.db")
head(eg)


## ----idType--------------------------------------------------------------
idType("org.Hs.eg.db")


## ----bitr2---------------------------------------------------------------
ids <- bitr(x, fromType="SYMBOL", toType=c("UNIPROT", "ENSEMBL"), annoDb="org.Hs.eg.db")
head(ids)


## ----groupGO-------------------------------------------------------------
library("DOSE")
data(geneList)
gene <- names(geneList)[abs(geneList) > 2]
head(gene)
ggo <- groupGO(gene     = gene,
               organism = "human",
               ont      = "BP",
               level    = 3,
               readable = TRUE)
head(summary(ggo))


## ----enrichGO------------------------------------------------------------
ego <- enrichGO(gene          = gene,
                universe      = names(geneList),
                organism      = "human",
                ont           = "CC",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.01,
                qvalueCutoff  = 0.05,
                readable      = TRUE)
head(summary(ego))


## ----gseGO---------------------------------------------------------------
ego2 <- gseGO(geneList     = geneList,
              organism     = "human",
              ont          = "CC",
              nPerm        = 100,
              minGSSize    = 120,
              pvalueCutoff = 0.01,
              verbose      = FALSE)
head(summary(ego2))


## ----enrichKEGG----------------------------------------------------------
kk <- enrichKEGG(gene         = gene,
                 organism     = "human",
                 pvalueCutoff = 0.05, 
                 readable     = TRUE,
                 use_internal_data = TRUE)
head(summary(kk))


## ----gseKEGG-------------------------------------------------------------
kk2 <- gseKEGG(geneList     = geneList,
               organism     = "human",
               nPerm        = 100,
               minGSSize    = 120,
               pvalueCutoff = 0.01,
               verbose      = FALSE,
               use_internal_data = TRUE)
head(summary(kk2))


## ----enrichDAVID, eval=FALSE---------------------------------------------
## david <- enrichDAVID(gene = gene,
##                      idType = "ENTREZ_GENE_ID",
##                      listType = "Gene",
##                      annotation = "KEGG_PATHWAY")


## ----barplot, fig.height=5, fig.width=6----------------------------------
barplot(ggo, drop=TRUE, showCategory=12)


## ----barplot-enrich, fig.height=5, fig.width=8---------------------------
barplot(ego, showCategory=8)


## ----enrichMap, fig.cap="enrichment map of enrichment result", fig.align="center", fig.height=16, fig.width=16, out.width="0.9\\textwidth", fig.pos="h"----
enrichMap(ego)


## ----cnetplot, fig.height=14, fig.width=14-------------------------------
cnetplot(ego, categorySize="pvalue", foldChange=geneList)


## ----cnetplot-KEGG, fig.height=14, fig.width=14--------------------------
cnetplot(kk, categorySize="geneNum", foldChange=geneList)


## ----gseaplot, fig.cap="plotting gsea result", fig.align="center", fig.height=6, fig.width=8, out.width="0.6\\textwidth", fig.pos="h"----
gseaplot(kk2, geneSetID = "hsa04145")


## ----viewKEGG, eval=FALSE------------------------------------------------
## library("pathview")
## hsa04110 <- pathview(gene.data  = geneList,
##                      pathway.id = "hsa04110",
##                      species    = "hsa",
##                      limit      = list(gene=max(abs(geneList)), cpd=1))


## ----gcSample------------------------------------------------------------
data(gcSample)
lapply(gcSample, head)


## ----comparecluster------------------------------------------------------
ck <- compareCluster(geneCluster = gcSample, fun = "enrichKEGG", use_internal_data = TRUE)
head(summary(ck))


## ----formula-------------------------------------------------------------
## formula interface
mydf <- data.frame(Entrez=c('1', '100', '1000', '100101467',
                       '100127206', '100128071'),
                   group = c('A', 'A', 'A', 'B', 'B', 'B'),
                   othergroup = c('good', 'good', 'bad', 'bad',
                       'good', 'bad'))
xx.formula <- compareCluster(Entrez~group, data=mydf, fun='groupGO')
head(summary(xx.formula))

## formula interface with more than one grouping variable
xx.formula.twogroups <- compareCluster(Entrez~group+othergroup,
                                       data=mydf, fun='groupGO')
head(summary(xx.formula.twogroups))


## ----compareCluster, fig.height=8, fig.width=8---------------------------
plot(ck)


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