## ----style, echo = FALSE, results = 'asis'-------------------------------
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE"))
)
options(width = 75)


## ------------------------------------------------------------------------
BiocManager::available("^org\\.")


## ---- message = FALSE----------------------------------------------------
library(AnnotationHub)

## ------------------------------------------------------------------------
query(AnnotationHub(), "^org\\.")


## ---- message = FALSE----------------------------------------------------
library(org.Hs.eg.db)


## ------------------------------------------------------------------------
head(keys(org.Hs.eg.db))


## ------------------------------------------------------------------------
eid <- sample(keys(org.Hs.eg.db), 10)


## ------------------------------------------------------------------------
mapIds(org.Hs.eg.db, eid, "SYMBOL", "ENTREZID")


## ------------------------------------------------------------------------
map <- select(org.Hs.eg.db, eid, c("SYMBOL", "GO"), "ENTREZID")
dim(map)
head(map)


## ---- message = FALSE----------------------------------------------------
library(GO.db)


## ---- message=FALSE------------------------------------------------------
library(dplyr)    # for `%>%`


## ------------------------------------------------------------------------
BiocManager::available("^TxDb") %>%
    tibble::enframe(name = NULL)


## ------------------------------------------------------------------------
query(AnnotationHub(), "^TxDb\\.")


## ---- message = FALSE----------------------------------------------------
library(TxDb.Hsapiens.UCSC.hg38.knownGene)


## ------------------------------------------------------------------------
exons(TxDb.Hsapiens.UCSC.hg38.knownGene)


## ------------------------------------------------------------------------
ex <- exons(TxDb.Hsapiens.UCSC.hg38.knownGene, columns = "GENEID")
ex


## ------------------------------------------------------------------------
std_ex <- keepStandardChromosomes(ex, pruning.mode="coarse")
std_ex


## ------------------------------------------------------------------------
table(seqnames(std_ex))


## ------------------------------------------------------------------------
std_ex[width(std_ex) > 10000]


## ---- message = FALSE----------------------------------------------------
library(ensembldb)

## ------------------------------------------------------------------------
query(AnnotationHub(), c("^EnsDb\\.", "Ensembl 96"))


## ---- message = FALSE----------------------------------------------------
library(biomaRt)


## ----biomart, eval=FALSE-------------------------------------------------
## library(biomaRt)
## head(listMarts(), 3)                      ## list marts
## head(listDatasets(useMart("ensembl")), 3) ## mart datasets
## ensembl <-                                ## fully specified mart
##     useMart("ensembl", dataset = "hsapiens_gene_ensembl")
## 
## head(listFilters(ensembl), 3)             ## filters
## myFilter <- "chromosome_name"
## substr(filterOptions(myFilter, ensembl), 1, 50) ## return values
## myValues <- c("21", "22")
## head(listAttributes(ensembl), 3)          ## attributes
## myAttributes <- c("ensembl_gene_id","chromosome_name")
## 
## ## assemble and query the mart
## res <- getBM(attributes =  myAttributes, filters =  myFilter,
##              values =  myValues, mart = ensembl)


## ---- message = FALSE----------------------------------------------------
library(KEGGREST)


## ---- message = FALSE----------------------------------------------------
library(AnnotationHub)
ah <- AnnotationHub()


## ------------------------------------------------------------------------
query(ah, "^org\\.")


## ------------------------------------------------------------------------
ah["AH70563"]


## ------------------------------------------------------------------------
org <- ah[["AH70563"]]
org


## ------------------------------------------------------------------------
chooseCentralOrgPkgSymbol(org)
columns(org)


## ---- message = FALSE----------------------------------------------------
library(dplyr)    # for `%>%`


## ------------------------------------------------------------------------
eid <- head(keys(org))
AnnotationDbi::select(org, eid, "SYMBOL", "ENTREZID")
eid %>%
    mapIds(x = org, "SYMBOL", "ENTREZID") %>%
    tibble::enframe("ENTREZID", "SYMBOL")


## ---- message = FALSE----------------------------------------------------
library(ExperimentHub)
library(curatedTCGAData)


## ------------------------------------------------------------------------
curatedTCGAData()
curatedTCGAData("BRCA")
curatedTCGAData("BRCA", c("RNASeqGene", "CNVSNP"))


## ---- message = FALSE----------------------------------------------------
mae <- curatedTCGAData("BRCA", c("RNASeqGene", "CNVSNP"), dry.run=FALSE)
mae


## ------------------------------------------------------------------------
mae[["BRCA_RNASeqGene-20160128"]] %>%
    assay() %>%
    colSums() %>%
    density() %>%
    plot(main = "TCGA BRCA RNASeq Library Size")


## ---- message = FALSE----------------------------------------------------
library(VariantAnnotation)


## ---- message = FALSE----------------------------------------------------
library(ensemblVEP)


## ------------------------------------------------------------------------
sessionInfo()