addband2gene.R

## add cytoband to gene
addband2gene = function(df,geneid = "ensembl_gene_id")
{
  if(!exists("anno_gene"))
  {
    ensembl <- biomaRt::useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl")
    anno_gene <<- biomaRt::getBM(attributes = c("ensembl_gene_id","external_gene_name","chromosome_name","start_position","end_position","band", "gene_biotype"),mart=ensembl )
  print("defined anno_gene")
  }
  if(geneid != "ensembl_gene_id") names(df)[names(df)==geneid] = "ensembl_gene_id" ## this is an ugly workaround - need to find a way to use rename_ for this but don't know how to specify a string instead of name in rename(geneid = "ensembl_gene_id")
  df = df %>% left_join(anno_gene, by=c( "ensembl_gene_id" ))
  if(geneid != "ensembl_gene_id") names(df)[names(df)=="ensembl_gene_id"] = geneid
  df %>% mutate(cytoband = paste0(chromosome_name,band))
}