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

## ----loadGenomicFeatures-------------------------------------------------
library("GenomicFeatures")

## ----loadDb--------------------------------------------------------------
samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                          package="GenomicFeatures")
txdb <- loadDb(samplefile)
txdb

## ----loadPackage---------------------------------------------------------
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene #shorthand (for convenience)
txdb

## ----seqlevels-----------------------------------------------------------
head(seqlevels(txdb))

## ----seqlevels2----------------------------------------------------------
seqlevels(txdb) <- "chr1"

## ----seqlevels3----------------------------------------------------------
seqlevels(txdb) <- seqlevels0(txdb)

## ----seqlevels4----------------------------------------------------------
seqlevels(txdb) <- "chr15"

## ----selectExample-------------------------------------------------------
keys <- c("100033416", "100033417", "100033420")
columns(txdb)
keytypes(txdb)
select(txdb, keys = keys, columns="TXNAME", keytype="GENEID")

## ----selectExercise------------------------------------------------------
columns(txdb)
cols <- c("TXNAME", "TXSTRAND", "TXCHROM")
select(txdb, keys=keys, columns=cols, keytype="GENEID")

## ----transcripts1--------------------------------------------------------
GR <- transcripts(txdb)
GR[1:3]

## ----transcripts2--------------------------------------------------------
GR <- transcripts(txdb, filter=list(tx_chrom = "chr15", tx_strand = "+"))
length(GR)
unique(strand(GR))

## ----exonsExer1----------------------------------------------------------
EX <- exons(txdb)
EX[1:4]
length(EX)
length(GR)

## ----transcriptsBy-------------------------------------------------------
GRList <- transcriptsBy(txdb, by = "gene")
length(GRList)
names(GRList)[10:13]
GRList[11:12]

## ----exonsBy-------------------------------------------------------------
GRList <- exonsBy(txdb, by = "tx")
length(GRList)
names(GRList)[10:13]
GRList[[12]]

## ----internalID----------------------------------------------------------
GRList <- exonsBy(txdb, by = "tx")
tx_ids <- names(GRList)
head(select(txdb, keys=tx_ids, columns="TXNAME", keytype="TXID"))

## ----introns-UTRs--------------------------------------------------------
length(intronsByTranscript(txdb))
length(fiveUTRsByTranscript(txdb))
length(threeUTRsByTranscript(txdb))

## ----extract-------------------------------------------------------------
library(BSgenome.Hsapiens.UCSC.hg19)
tx_seqs1 <- extractTranscriptSeqs(Hsapiens, TxDb.Hsapiens.UCSC.hg19.knownGene,
                                  use.names=TRUE)

## ----translate1----------------------------------------------------------
suppressWarnings(translate(tx_seqs1))

## ----betterTranslation---------------------------------------------------
cds_seqs <- extractTranscriptSeqs(Hsapiens,
                                  cdsBy(txdb, by="tx", use.names=TRUE))
translate(cds_seqs)

## ----supportedUCSCtables-------------------------------------------------
supportedUCSCtables(genome="mm9")

## ----makeTxDbFromUCSC, eval=FALSE----------------------------------------
## mm9KG_txdb <- makeTxDbFromUCSC(genome="mm9", tablename="knownGene")

## ----discoverChromNames--------------------------------------------------
head(getChromInfoFromUCSC("hg19"))

## ----makeTxDbFromBiomart, eval=FALSE-------------------------------------
## mmusculusEnsembl <- makeTxDbFromBiomart(dataset="mmusculus_gene_ensembl")

## ----saveDb-1, eval=FALSE------------------------------------------------
## saveDb(mm9KG_txdb, file="fileName.sqlite")

## ----loadDb-1, eval=FALSE------------------------------------------------
## mm9KG_txdb <- loadDb("fileName.sqlite")

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