## 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 database form a GFF file from Ensembl.
## ftp://ftp.ensembl.org/pub/release-83/gff3/rattus_norvegicus
gff <- "Rattus_norvegicus.Rnor_6.0.83.gff3.gz"
DB <- ensDbFromGff(gff=gff)
edb <- EnsDb(DB)
edb
## 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))
## load the DB file directly
EDB <- EnsDb(DB)
## Alternatively, we could fetch a GTF file directly from AnnotationHub
## and build the database from that:
library(AnnotationHub)
ah <- AnnotationHub()
## Query for all GTF files from Ensembl for Ensembl version 81
query(ah, c("Ensembl", "release-81", "GTF"))
## We could get the one from e.g. Bos taurus:
DB <- ensDbFromAH(ah["AH47941"])
edb <- EnsDb(DB)
edb
## 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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