chr1swallace/coloc

coloc.detail, coloc.process function not found (coloc 5.1.2)

Opened this issue · 5 comments

zillurbmb51 commented

Hi I have installed coloc as follows:

install_github("chr1swallace/coloc@main",build_vignettes=F)

If I use "build_vignettes=T" I got the following error:

   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'coloc' from GitHub:
  System command 'R' failed, exit status: 1, stdout & stderr were printed

But it works fine for "coloc.abf" or other functions.

> library(coloc)
This is coloc version 5.1.2
> coloc.detail()
Error in coloc.detail() : could not find function "coloc.detail"
> coloc.process()
Error in coloc.process() : could not find function "coloc.process"

But I need the coloc.detail or coloc.process function to do the sensitivity test, right? Here is the reference for sensitivity function:
sensitivity_function_coloc

Any help?

chr1swallace commented
zillurbmb51 commented

@chr1swallace Thank you.

I have tried to use coloc.abf() output for sensitivity. Probably, it works. But getting the following error message.
Why I am getting this error?

> myres2=coloc.abf(dataset1 = scz5,dataset2 = eoso5,p12 = 1e-6)
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf 
 0.00e+00  0.00e+00  9.33e-32  1.00e+00  2.07e-32 
[1] "PP abf for shared variant: 2.07e-30%"
There were 13 warnings (use warnings() to see them)
> sb2=sensitivity(myres2,dataset1 = scz5,dataset2 = eoso5,rule = 'H4>0.1')
Results fail decision rule H4>0.1
Error in matrix(f(p12), nrow = nrow(pr1), ncol = ncol(pr1), byrow = TRUE) : 
  'data' must be of a vector type, was 'NULL'
chr1swallace commented
zillurbmb51 commented

Thank you.

That would be so kind of you.

chr1swallace commented

would it be possible for you to share (subsets of) your data so I can find out why this happens?