View source: R/feature-synonym.R
Build a reference set of genes and synonym at a given featureset_id. Need paths to <hugo/hgnc_complete_set.txt> for annotation info (param: gene_annotation_file_path) and <grch38_release85_homosap_gene/newGene.tsv> as gene location info (param: gene_location_file_path)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | build_reference_gene_set(
featureset_id,
gene_annotation_file_path = NULL,
gene_location_file_path = NULL,
alias_fields = c("hgnc_id", "symbol", "alias_symbol", "prev_symbol", "entrez_id",
"ensembl_gene_id", "vega_id", "ucsc_id", "ena", "refseq_accession", "ccds_id",
"uniprot_ids", "pubmed_id", "mgd_id", "rgd_id", "cosmic", "omim_id", "mirbase",
"homeodb", "snornabase", "bioparadigms_slc", "orphanet", "pseudogene.org",
"horde_id", "merops", "imgt", "iuphar", "kznf_gene_catalog", "mamit.trnadb", "cd",
"lncrnadb", "enzyme_id", "intermediate_filament_db"),
hierarchy = c("ensembl_gene_id", "vega_id", "ucsc_id", "ccds_id", "gene_symbol",
"hgnc_id"),
con = NULL
)
|
featureset_id |
FeatureSet id at which to build a reference gene set |
gene_annotation_file_path |
file providing annotation info (e.g. <hugo/hgnc_complete_set.txt>) |
gene_location_file_path |
gene location info (e.g. <grch38_release85_homosap_gene/newGene.tsv>) |
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