Get Genome Annotation

Extract the genome annotation.

get_annotation(experiment)

Arguments

experiment	TSRexploreR object.

Value

TxDb object of genome annotation.

See also

get_assembly to get genome assembly.

Examples

annotation <- system.file("extdata", "S288C_Annotation.gtf", package="TSRexploreR")
exp <- tsr_explorer(genome_annotation=annotation)
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> Warning: The "phase" metadata column contains non-NA values for features of type
#>   stop_codon. This information was ignored.
#> OK

get_annotation(exp)
#> TxDb object:
#> # Db type: TxDb
#> # Supporting package: GenomicFeatures
#> # Data source: /tmp/RtmpTsVxFl/temp_libpath66d16d6b7269/TSRexploreR/extdata/S288C_Annotation.gtf
#> # Organism: NA
#> # Taxonomy ID: NA
#> # miRBase build ID: NA
#> # Genome: NA
#> # Nb of transcripts: 7127
#> # Db created by: GenomicFeatures package from Bioconductor
#> # Creation time: 2021-04-04 22:44:56 -0400 (Sun, 04 Apr 2021)
#> # GenomicFeatures version at creation time: 1.42.0
#> # RSQLite version at creation time: 2.2.4
#> # DBSCHEMAVERSION: 1.2