## ----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----------------------------------------------------------
txdb <- restoreSeqlevels(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, vals <- 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)


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


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


## ----supportedUCSCtables-------------------------------------------------
supportedUCSCtables()[1:4, ]

## ----makeTxDbFromUCSC, eval=FALSE----------------------------------------
## mm9KG <- makeTxDbFromUCSC(genome = "mm9", tablename = "knownGene")


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


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


## ----saveDb-1, eval=FALSE------------------------------------------------
## saveDb(mm9KG, file="fileName.sqlite")


## ----loadDb-1, eval=FALSE------------------------------------------------
## mm9KG <- loadDb("fileName.sqlite")


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