retrieveHgncGeneList: Retrieve gene identifiers from HGNC

In luannnguyen/hmfGeneAnnotation: Determines gene amplifications and biallelic losses from HMF pipeline output

Description

Retrieve gene identifiers from HGNC

Usage

retrieveHgncGeneList(
 
    hgnc.url = "https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_prev_sym&col=gd_aliases&col=gd_pub_ensembl_id&status=Approved&hgnc_dbtag=on&order_by=gd_app_sym_sort&format=text&submit=submit",
  out.path = NULL,
  export.as.rdata = F,
  verbose = T,
  ...
)

Arguments

hgnc.url	URL to HGNC database, where the output contains the columns: HGNC ID, Approved symbol, Previous symbols, Synonyms, ENSEMBL gene id
out.path	Export path
export.as.rdata	Save as RData file?
verbose	Show messages?
...	Arguments that can be passed to biomaRt::useMart()

Value

A dataframe of gene identifers from HGNC

luannnguyen/hmfGeneAnnotation documentation built on May 6, 2020, 1:07 p.m.