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

Using coloc for conditionally independent eQTLs in the HLA region

It could work, if​ you trust your conditional analysis (is this with summary data or original genotypes?) You could also look at hypercoloc to group the multiple signals -- https://chr1swallace.github.io...

Using coloc for conditionally independent eQTLs in the HLA region

If you have original genotypes I would run Susie directly on that, particularly in the mhc. I don't thinki have a function yet to work with Susie output but it...

coloc.abf result: unexpectedly high PP.H4.abf

Could you show me what the data look like? Agree this shouldn't happen if your p values accurate. If you do pnorm(-abs(beta)/sqrt(varbeta), lower=FALSE)*2, are they the p values you expect?...

N argument missing when calling susieR::susie_rss()

thank you for the bug report. I can't reproduce this with my example data though. I did just fix a different bug to do with passing the sample size to...

N argument missing when calling susieR::susie_rss()

thanks. I'll try to push a new version to CRAN. -- https://chr1swallace.github.io ________________________________ From: zy8281263 ***@***.***> Sent: Friday, May 12, 2023 8:38 AM To: chr1swallace/coloc ***@***.***> Cc: Chris Wallace ***@***.***>;...

N argument missing when calling susieR::susie_rss()

Can you check whether it converges in more iterations? -- https://chr1swallace.github.io ________________________________ From: Junhao WEN ***@***.***> Sent: Thursday, June 8, 2023 9:21:40 PM To: chr1swallace/coloc ***@***.***> Cc: Chris Wallace ***@***.***>;...

N argument missing when calling susieR::susie_rss()

Did you check the consistency of the LD matrix as suggested? This is a Susie error, that can arise when the LD is calculated from a population that is not...

N argument missing when calling susieR::susie_rss()

runsusie is just a wrapper around susie_rss that 1. accepts data in the same format as other coloc functions 2. calls susie_rss 3. annotates the output of susie_rss with snp...

GWAS-GWAS colocalisation

We looked at this for quantitative traits and concluded that while mathematically incorrect, it was fine in practice as long as you had medium- large sample sizes https://academic.oup.com/nar/article/48/6/2866/5766659 Not published,...

GWAS-GWAS colocalisation

This paper has results from quantitative traits, but we never published the case control studies https://academic.oup.com/nar/article/48/6/2866/5766659 -- https://chr1swallace.github.io ________________________________ From: Junhao WEN ***@***.***> Sent: Friday, June 23, 2023 4:21:00 PM...