FANTOM CAT distributes, next to the GTF, an ID mapping table
(geneID, transcriptID, CAGEClusterID) and a gene information table
(geneClass, geneCategory, TIEScore_tier, splicingType,
directionality, transposable element associations, ...). This function
joins them into the annotation directory: the CAGE cluster (the
CAGE-defined promoter of each transcript) becomes cage_cluster_id, with
its coordinates parsed into cage_cluster_seqid, cage_cluster_start,
cage_cluster_end, and the gene information columns are added to the
gene table in snake case. See download_fantom_cat_tables().
Arguments
- x
An annotation directory path or an IsoformicExperiment.
- id_mapping
Path (or data frame) of the ID mapping table.
- gene_info
Optional path (or data frame) of the gene info table.
Examples
if (FALSE) { # \dontrun{
gtf <- download_reference(reference = "fantom", version = "lv3_robust")
tables <- download_fantom_cat_tables("lv3_robust")
annot <- prepare_isoformic_annotation(gtf)
add_fantom_cat_tables(annot, tables[["id_mapping"]], tables[["gene_info"]])
} # }