CBIIT/LDlinkR

LDproxy_batch

Closed this issue · 4 comments

cs16436 commented

Hi,

I've been using LDproxy_batch, which is an excellent tool! When I previously used this, the outputs included a column 'query_snp'. I've noticed that recent outputs no longer include this column:

Function RS_Number Coord Alleles MAF Distance Dprime R2 Correlated_Alleles FORGEdb RegulomeDB

Please may I check that this column is no longer included (or if there may be an issue with my outputs)?

Thank you very much in advance!

timyers commented

Hello,

Thank you for reaching out and thanks for your interest in LDlinkR. I ran a test and my output includes the 'query_snp' column. Here's the example:

LDproxy_batch(snp = c("rs114", "rs127"), token = Sys.getenv("LDLINK_TOKEN"), append = TRUE, genome_build = "grch38" )

We did have an issue a while back with columns in the output from LDproxy but we were able to fix it. Are you using the latest version of LDlinkR, v1.2.3? If not, please update and try again. Also, the 'query_snp' column is only added to the output file when 'append = TRUE'. If you are still having trouble, please provide us with a reproducible example of your code and I'll try to provide additional help.

Kind regards,
Tim

machiela commented
  • 👍1
cs16436 commented

Hi Tim,

Thank you so much for your help - installing the latest version of LDlinkR did fix this.

Best wishes, Chloe

  • 👍1
timyers commented

That's great news! Glad we were able to help.
Best of luck with your research.
Regards,
Tim