build_reference_gene_set: Build a reference gene set at user specified FeatureSet id

Description Usage Arguments

View source: R/feature-synonym.R

Description

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)

Usage

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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
)

Arguments

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>)


Paradigm4/revealgenomics documentation built on April 7, 2020, 2:01 a.m.