Chris Wallace

icon indicating a website link http://chr1swallace.github.io

icon company University of Cambridge icon location Cambridge, UK icon location Statisitician using genomics to understand immune-mediated diseases. Github hosts mainly R packages to do statistical analysis of genetic data.

Results 48 comments of Chris Wallace

length of snp vector should be 1 less than ncol(res$lbf_variable)

It's not your data, sorry. I moved some code to help a user with a specific request and silently broke something. Now fixed. Could I ask you to download afresh...

length of snp vector should be 1 less than ncol(res$lbf_variable)

so sorry, I failed to push the change to github. try again? -- https://chr1swallace.github.io ________________________________ From: shannjiang ***@***.***> Sent: Tuesday, August 22, 2023 7:02 PM To: chr1swallace/coloc ***@***.***> Cc: Chris...

coloc.abf

Each dataset needs a snp identifier. Yours doesn't have one. -- https://chr1swallace.github.io ________________________________ From: MoMaz123 ***@***.***> Sent: Tuesday, September 26, 2023 4:56:38 PM To: chr1swallace/coloc ***@***.***> Cc: Subscribed ***@***.***> Subject:...

Why is the PP.H4.abf result of res$summary different from the maximum PP.H4 in res$results?

PP.H4 is explained here https://chr1swallace.github.io/coloc/articles/a03_enumeration.html does that help? -- https://chr1swallace.github.io ________________________________ From: dqq0404 ***@***.***> Sent: Friday, April 12, 2024 7:08:23 AM To: chr1swallace/coloc ***@***.***> Cc: Subscribed ***@***.***> Subject: [chr1swallace/coloc] Why...

Error in coloc.susie ()

I can't help unless you show me what your input data looks like -- https://chr1swallace.github.io ________________________________ From: Huiflorazhan ***@***.***> Sent: Friday, April 12, 2024 2:52:03 AM To: chr1swallace/coloc ***@***.***> Cc:...

Error when running COLOC

The dataset is supposed to be a list, not a data frame. There should be a single value for type, not one for each SNP. This is to emphasise that...

How to interpret the results of susie summary？

I just replied to you asking the same question in issue #87. Susie appears to have found 10 distinct signals for trait 1 and 7 for trait 2. coloc then...

How to interpret the results of susie summary？

My strong advice is to check that your Susie results make sense. I doubt you have so many casual variants really. I fear your LD matrix is not a good...

object 'LD' not found in installation (build_vignettes=TRUE)

I'll take a look at this next week. Meantime you could install from CRAN which is pretty up to date. -- https://chr1swallace.github.io ________________________________ From: Jundong LIU ***@***.***> Sent: Saturday, July...

object 'LD' not found in installation (build_vignettes=TRUE)

Thanks. You can view the vignette here till I fix the issue. https://chr1swallace.github.io/coloc/articles/a06_SuSiE.html -- https://chr1swallace.github.io ________________________________ From: Jundong LIU ***@***.***> Sent: Saturday, July 15, 2023 4:21:15 PM To: chr1swallace/coloc ***@***.***>...