search

waldronlab / HGNChelper

Identify and correct invalid gene symbols
https://waldronlab.io/HGNChelper/
55 stars 9 forks source link

getCurrentMap() returns HTTP status was '404 Not Found' #1

Closed kcs3 closed 5 years ago

kcs3 commented 5 years ago

Version: 0.5.2 Date: 2018-07-05

library(HGNChelper) new.hgnc.table <- getCurrentHumanMap() Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open URL 'http://www.genenames.org/cgi-bin/hgnc_downloads?col=gd_hgnc_id&col=gd_app_sym&col=gd_prev_sym&col=gd_aliases&status=Approved&status=Entry+Withdrawn&status_opt=2&where=&order_by=gd_hgnc_id&format=text&limit=&hgnc_dbtag=on&submit=submit': HTTP status was '404 Not Found'

lwaldron commented 5 years ago

Thanks @kcs3. The HGNC seems to have changed their downloads page. Working on finding the right data again.

kcs3 commented 5 years ago

Thanks, good luck!

lwaldron commented 5 years ago

I think this is resolved in 0beff7d (version 0.7.0). The HGNC map is bigger now, I think because the file I use now includes symbols for non-coding RNA, pseudogenes, and some other things (see the "Locus type" help at genenames.org). @kcs3 I would really appreciate it if you could give it a try here and let me know if it passes your sanity check before I upload to CRAN.

lwaldron commented 5 years ago

Resolved with 0beff7d15c748f44f276636e48033ad8f750ea2d, release 0.7.1 was submitted to CRAN this morning.