## ----doeval, echo = FALSE, results = "hide"--------------------------------
## Globally switch off execution of code chunks
evalMe <- FALSE
haveProt <- FALSE

## ----loadlib, message = FALSE, eval = evalMe-------------------------------
#  library(ensembldb)
#  library(EnsDb.Hsapiens.v75)
#  edb <- EnsDb.Hsapiens.v75
#  ## Evaluate whether we have protein annotation available
#  hasProteinData(edb)

## ----listCols, message = FALSE, eval = evalMe------------------------------
#  listTables(edb)

## ----haveprot, echo = FALSE, results = "hide", eval = evalMe---------------
#  ## Use this to conditionally disable eval on following chunks
#  haveProt <- hasProteinData(edb) & evalMe

## ----a_transcripts, eval = haveProt----------------------------------------
#  ## Get also protein information for ZBTB16 transcripts
#  txs <- transcripts(edb, filter = GenenameFilter("ZBTB16"),
#  		   columns = c("protein_id", "uniprot_id", "tx_biotype"))
#  txs

## ----a_transcripts_coding_noncoding, eval = haveProt-----------------------
#  ## Subset to transcripts with tx_biotype other than protein_coding.
#  txs[txs$tx_biotype != "protein_coding", c("uniprot_id", "tx_biotype",
#  					  "protein_id")]

## ----a_transcripts_coding, eval = haveProt---------------------------------
#  ## List the protein IDs and uniprot IDs for the coding transcripts
#  mcols(txs[txs$tx_biotype == "protein_coding",
#  	  c("tx_id", "protein_id", "uniprot_id")])

## ----a_transcripts_coding_up, eval = haveProt------------------------------
#  ## List all uniprot mapping types in the database.
#  listUniprotMappingTypes(edb)
#  
#  ## Get all protein_coding transcripts of ZBTB16 along with their protein_id
#  ## and Uniprot IDs, restricting to protein_id to uniprot_id mappings based
#  ## on "DIRECT" mapping methods.
#  txs <- transcripts(edb, filter = list(GenenameFilter("ZBTB16"),
#  				      UniprotMappingTypeFilter("DIRECT")),
#  		   columns = c("protein_id", "uniprot_id", "uniprot_db"))
#  mcols(txs)

## ----a_genes_protdomid_filter, eval = haveProt-----------------------------
#  ## Get all genes that encode a transcript encoding for a protein that contains
#  ## a certain protein domain.
#  gns <- genes(edb, filter = ProtDomIdFilter("PS50097"))
#  length(gns)
#  
#  sort(gns$gene_name)

## ----a_2_annotationdbi, message = FALSE, eval = haveProt-------------------
#  ## Show all columns that are provided by the database
#  columns(edb)
#  
#  ## Show all key types/filters that are supported
#  keytypes(edb)

## ----a_2_select, message = FALSE, eval = haveProt--------------------------
#  select(edb, keys = "ZBTB16", keytype = "GENENAME",
#         columns = "UNIPROTID")

## ----a_2_select_nmd, message = FALSE, eval = haveProt----------------------
#  ## Call select, this time providing a GenenameFilter.
#  select(edb, keys = GenenameFilter("ZBTB16"),
#         columns = c("TXBIOTYPE", "UNIPROTID", "PROTEINID"))

## ----b_proteins, message = FALSE, eval = haveProt--------------------------
#  ## Get all proteins and return them as an AAStringSet
#  prts <- proteins(edb, filter = GenenameFilter("ZBTB16"),
#  		 return.type = "AAStringSet")
#  prts

## ----b_proteins_mcols, message = FALSE, eval = haveProt--------------------
#  mcols(prts)

## ----b_proteins_prot_doms, message = FALSE, eval = haveProt----------------
#  ## Get also protein domain annotations in addition to the protein annotations.
#  pd <- proteins(edb, filter = GenenameFilter("ZBTB16"),
#  	       columns = c("tx_id", listColumns(edb, "protein_domain")),
#  	       return.type = "AAStringSet")
#  pd

## ----b_proteins_prot_doms_2, message = FALSE, eval = haveProt--------------
#  ## The number of protein domains per protein:
#  table(names(pd))
#  
#  ## The mcols
#  mcols(pd)