A function that generates a HTML link for selected identifiers (DBSNP, COSMIC, CLINVAR, ENTREZ) — generate_annotation_link • PCGR

A function that generates a HTML link for selected identifiers (DBSNP, COSMIC, CLINVAR, ENTREZ)

Usage

generate_annotation_link(
  var_df,
  vardb = "DBSNP",
  vartype = "snv_indel",
  group_by_var = c("VAR_ID", "ENTREZGENE"),
  url_prefix = "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=",
  link_key_var = "DBSNP_RSID",
  link_display_var = "DBSNP_RSID"
)

Arguments

var_df: data frame
vardb: type of database
vartype: 'snv_indel' or 'cna'
group_by_var: variable used for grouping (VAR_ID)
url_prefix: url prefix for link generation
link_key_var: variable used in url for linking
link_display_var: variable used in url for display

Value

df_annotation_links