## Not run:
#
# ## get all human gene/transcript/exon annotations from Ensembl (75)
# ## the resulting tables will be stored by default to the current working
# ## directory; if the correct Ensembl api (version 75) is defined in the
# ## PERL5LIB environment variable, the ensemblapi parameter can also be omitted.
# fetchTablesFromEnsembl(75,
# ensemblapi="/home/bioinfo/ensembl/75/API/ensembl/modules",
# species="human")
#
# ## These tables can then be processed to generate a SQLite database
# ## containing the annotations
# DBFile <- makeEnsemblSQLiteFromTables()
#
# ## and finally we can generate the package
# makeEnsembldbPackage(ensdb=DBFile, version="0.0.1",
# maintainer="Johannes Rainer <johannes.rainer@eurac.edu>",
# author="J Rainer")
#
# ## Build an annotation file from a GTF file.
# ## the GTF file can be downloaded from
# ## ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/
# gtffile <- "Homo_sapiens.GRCh37.75.gtf.gz"
# ## generate the SQLite database file
# DB <- ensDbFromGtf(gtf=paste0(ensemblhost, gtffile), verbose=TRUE)
#
# ## load the DB file directly
# EDB <- EnsDb(DB)
#
# ## End(Not run)
## Generate a sqlite database for genes encoded on chromosome Y
chrY <- system.file("chrY", package="ensembldb")
DBFile <- makeEnsemblSQLiteFromTables(path=chrY ,dbname=tempfile())
## load this database:
edb <- EnsDb(DBFile)
edb
## Generate a sqlite database from a GRanges object specifying
## genes encoded on chromosome Y
load(system.file("YGRanges.RData", package="ensembldb"))
Y
DB <- ensDbFromGRanges(Y, path=tempdir(), version=75,
organism="Homo_sapiens")
edb <- EnsDb(DB)
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