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PheWeb-UMich
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Matthew Maher
Apr 7
LD highlighting not working?
I'm just using pheweb for the first time (nice tool!) and everything's pretty much gone great
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LD highlighting not working?
I'm just using pheweb for the first time (nice tool!) and everything's pretty much gone great
Apr 7
jane Chang
Apr 7
GWAS is performed using logistic regression
Dear all, We are interested in "290: Delirium dementia and amnestic and other cognitive
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GWAS is performed using logistic regression
Dear all, We are interested in "290: Delirium dementia and amnestic and other cognitive
Apr 7
Matthew Maher
, …
Andy Boughton
4
Apr 5
LD highlighting
It's worth noting that LocusZoom matches LD information based on chrom/pos/ref/alt, not rsID. The
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LD highlighting
It's worth noting that LocusZoom matches LD information based on chrom/pos/ref/alt, not rsID. The
Apr 5
Charlie Repaci
11/11/22
Missing data for some tissues
Hello, One of our variants that should be showing up for all tissues only shows up for two in the
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Missing data for some tissues
Hello, One of our variants that should be showing up for all tissues only shows up for two in the
11/11/22
Suchen Zheng
,
Sarah Gagliano Taliun
2
10/31/22
Where to download all the summary statistic files?
wget should work! Le lundi 31 octobre 2022 à 15:38:12 UTC-4, sz...@yale.edu a écrit : Hello, If there
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Where to download all the summary statistic files?
wget should work! Le lundi 31 octobre 2022 à 15:38:12 UTC-4, sz...@yale.edu a écrit : Hello, If there
10/31/22
Charlie Repaci
,
Peter VandeHaar
2
7/28/22
rsid mapping
Huh, curious. What version of pheweb are you using? What did you set for “hg_build_number“ in config.
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rsid mapping
Huh, curious. What version of pheweb are you using? What did you set for “hg_build_number“ in config.
7/28/22
Joseph Chase
,
Peter VandeHaar
2
7/28/22
Specs on what this should take to run?
How many variants? How many phenotypes? I recommend loading on a big machine (50+ cores) or a cluster
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Specs on what this should take to run?
How many variants? How many phenotypes? I recommend loading on a big machine (50+ cores) or a cluster
7/28/22
Charlie Repaci
2
6/9/22
Error in QQ plots
I've figured out the issue! My teammate passed me a small subset of the data to work with which
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Error in QQ plots
I've figured out the issue! My teammate passed me a small subset of the data to work with which
6/9/22
Jennifer Huffman
,
pjvandehaar
2
10/3/21
effect allele when creating your own instance of PheWeb
Hi Jenny, PheWeb assumes that all of those are for the alternate allele. Thanks, I just updated the
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effect allele when creating your own instance of PheWeb
Hi Jenny, PheWeb assumes that all of those are for the alternate allele. Thanks, I just updated the
10/3/21
Mokerina Liao
,
Peter VandeHaar
2
8/4/21
how to generate/input phewas data
You need one file for each phenotype (ie, one file per GWAS). Section 3 of the instructions describes
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how to generate/input phewas data
You need one file for each phenotype (ie, one file per GWAS). Section 3 of the instructions describes
8/4/21
Shicheng Guo
,
Peter VandeHaar
2
7/14/21
Github web page
The Manhattan plot pages have a download link. See the top-right of https://pheweb.org/UKB-TOPMed/
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Github web page
The Manhattan plot pages have a download link. See the top-right of https://pheweb.org/UKB-TOPMed/
7/14/21
Shicheng Guo
,
Sarah Gagliano Taliun
2
7/9/21
Pheweb data download - summary statistics
Hi! Thanks for your interest in PheWeb. Below are the locations to download summary statistics for
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Pheweb data download - summary statistics
Hi! Thanks for your interest in PheWeb. Below are the locations to download summary statistics for
7/9/21
Michael Chong
,
pjvandehaar
2
6/19/21
Login Access outside of Google Accounts?
Here are options I can think of: 1. Your users can make google accounts connected to their non-google
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Login Access outside of Google Accounts?
Here are options I can think of: 1. Your users can make google accounts connected to their non-google
6/19/21
James Pirruccello
,
pjvh
2
3/10/21
Effect allele vs minor allele vs non-reference allele in PheWeb
Yeah, it sounds like you figured everything out correctly. You're right that for a variant "
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Effect allele vs minor allele vs non-reference allele in PheWeb
Yeah, it sounds like you figured everything out correctly. You're right that for a variant "
3/10/21
James Warren
,
Peter VandeHaar
4
2/19/21
upper bound on # of phenotypes?
Fantastic - thank you so much! On Friday, February 19, 2021 at 11:09:32 AM UTC-8 pjvh wrote: I added
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upper bound on # of phenotypes?
Fantastic - thank you so much! On Friday, February 19, 2021 at 11:09:32 AM UTC-8 pjvh wrote: I added
2/19/21
Fedik Rahimov
,
Peter VandeHaar
2
2/10/21
R code for PheWEB
I'm glad you like how pheweb's manhattan plots work! Unfortunately, I don't have any
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R code for PheWEB
I'm glad you like how pheweb's manhattan plots work! Unfortunately, I don't have any
2/10/21
Ashley Qin
,
pjvandehaar
2
2/2/21
Speed up "gather-pvalues-for-each-gene"
Sorry about getting back to you so late. Presumably you've figured it out by now. Yeah, that step
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Speed up "gather-pvalues-for-each-gene"
Sorry about getting back to you so late. Presumably you've figured it out by now. Yeah, that step
2/2/21
Pete Santos
,
Peter VandeHaar
2
8/21/20
Having difficult getting started / following the README does not seem to work
It looks like that was failing because there were no significant associations in that tiny test file,
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Having difficult getting started / following the README does not seem to work
It looks like that was failing because there were no significant associations in that tiny test file,
8/21/20
Sarah Gagliano Taliun
8/18/20
Welcome!
Hello. This group is for discussion of PheWeb. GitHub: https://github.com/statgen/pheweb Citation:
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Welcome!
Hello. This group is for discussion of PheWeb. GitHub: https://github.com/statgen/pheweb Citation:
8/18/20
