varemo/piano

Use tab-separator for scan?

Closed this issue · 5 comments

while(length(l<-scan(con,nlines=1,what="character",quiet=T)) > 0) {

As .gmt files are tab-delimited, shouldn't this scan be using sep = "\t"?

My .gmt file (http://download.baderlab.org/EM_Genesets/current_release/Mouse/symbol/Mouse_AllPathways_November_01_2017_symbol.gmt) was not parsed correctly by loadGSC(), but using sep = "\t" fixed it.

It has been working on other .gtm files that I have tested. But if it fails for the file you point that, that is certainly an issue! I will check this asap. Probably you are correct, regarding the sep = "\t", just need to verify that it works for all .gmt files. Thanks for reporting!

Thanks for looking at it!

Haven't forgotten about this, but got swamped with other work. Will get back to this after the holidays. I guess (hope) it is not a show stopper for you at this point anyways...

No problem for me, I made the change locally and it has been working fine for me since!

Thanks!

Now fixed and included in all branches! Should propagate to Bioconductor within a few days. Thanks again for pointing this out.