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By run the susie_rss( ) function of a locus GWAS, I have got the result of PIP and cs for each SNP.
1. The serial number of CS is how to order, for example, the 689th SNP in CS 1, whose PIP is 1, b…
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Hello,
I saw a few tickets reporting a similar issue when using:
./munge_sumstats.py \
--sumstats UKB.GWAS.txt \
--N 336974 \
--ignore BETA \
--out UKB_DR \
--merge-alleles w_hm3.snplist
…
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Dear Omeed,
When running MTAG on the GWAS results of two related traits (UKB data, phenotypic correlation 0.6), with sample overlap, I picked up some loci that were not significant in the GWAS. Ho…
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Hi Dr. Yuan,
I would like to use the PMR method in my analysis. Trying to use the following function with my data I got an error:
"Error Chol () decomposition failed"
PMR_summary_Egger(Zscore_1…
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Assuming proper separation of samples so that no sample information is shared between exposure and outcome instruments, is there any intrinsic problem with using MTAG output summary statistics as inst…
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Hi,
It would be great if you could add in a function to make stratified QQ plots. For instance stratified by bins of info-score (_e.g._ https://github.com/swvanderlaan/MetaGWASToolKit/blob/master/S…
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Hi,
I have GWAS summary data and individual level data in the same cohort, also have DNA methylation prediction models. I use GWAS summary data to run Predict.py, get the methylation-level associati…
ymqwa updated
2 years ago
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Hello,
I used MTAG to enhance the GWAS ability. I have phenotypic data of three environments of plant hegiht which has low repeatability. We call the rep_1,rep_2,rep_3. The GWAS signials were unde…
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Hi Sam,
I am following your plink PRS tutorial and I have a couple of questions re mismatching-snps section [https://choishingwan.github.io/PRS-Tutorial/target/#mismatching-snps](url) .
1. You s…
DM087 updated
2 years ago
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Hello @getian107 ,
Thank you very much for your great work with this software.
I have been experiencing some issues with long running time for PRS-CSx. I am using summary statistics of African and …