This function instantiates a ContextData object containing information
about the genomic context of transcripts.
It requires a GFF file for gene annotation and constructs a TxDb
object from it. The function also prepares an annotation table and
updates the transcript names in the TxDb object.
The ContextData object can then be used in conjunction with
IsoformicExperiment for transcriptomic analyses.
Usage
create_context_data(
gff_file,
...,
organism,
orgdb_package,
bsgenome_package,
tx_type_palette = NULL
)Arguments
- gff_file
Character string specifying the path to a GFF file containing the gene annotation.
- ...
These dots are for future extensions and must be empty.
- organism
Character string specifying the organism name (e.g., "Homo sapiens").
- orgdb_package
Character string specifying the name of the organism database package (e.g., "org.Hs.eg.db").
- bsgenome_package
Character string specifying the name of the BSgenome package (e.g., "BSgenome.Hsapiens.UCSC.hg38").
- tx_type_palette
Named Character vector specifying the color palette for transcript types.