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

[zillurbmb51]

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:

Any help?

[chr1swallace]

Hi, I'm currently on holiday, so can't test, but I think this is an issue with documentation. The coloc.detail function was removed, but coloc.abf() updated so that sensitivity() should work with its output. Could you give it a try?

https://chr1swallace.github.io

---

From: zillurbmb51 @.> Sent: Thursday, April 14, 2022 12:34:19 PM To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] coloc.detail, coloc.process function not found (coloc 5.1.2) (Issue #82)

Hi I have installed coloc as follows:

@.***",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]https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F12833907%2F163382703-5cbd807f-602c-42c4-a45f-86f3c566f992.png&data=04%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7C7d97918e79394e38142e08da1e0ab8bf%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637855328634339776%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=N0S7WnkytVUe3AciCr4z6WliQhmOpHOO073ken1loaw%3D&reserved=0

Any help?

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[zillurbmb51]

@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]

Mmm. I'm not sure. Will look at this when back at a computer

https://chr1swallace.github.io

---

From: zillurbmb51 @.> Sent: Thursday, April 14, 2022 2:11:24 PM To: chr1swallace/coloc @.> Cc: Chris Wallace @.>; Mention @.> Subject: Re: [chr1swallace/coloc] coloc.detail, coloc.process function not found (coloc 5.1.2) (Issue #82)

@chr1swallacehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fchr1swallace&data=04%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7Cbc157229b89c40b9dd3f08da1e185a4f%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637855387178544231%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=HtrYq2v1xGqAMVs6YCV6sAuLq8mvY7R42g3yYdPG4p4%3D&reserved=0 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'

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[zillurbmb51]

Thank you.

That would be so kind of you.

[chr1swallace]

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