User: Mahan
Mahan • 70
- Reputation:
- 70
- Status:
- Trusted
- Location:
- Taipei, Taiwan
- Website:
- https://www.mahanteshb...
- Twitter:
- Mahantesh19_
- Last seen:
- 2 days, 23 hours ago
- Joined:
- 5 years, 8 months ago
- Email:
- m******************@gmail.com
Epidemiology | Project Manager | Social Media Strategy | Digital Marketing | Hiker
Posts by Mahan
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... Is there any tool/package to obtain the gene names for the SNPs of my interest from a GWAS analysis? ...
written 28 days ago by
Mahan • 70
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... Hi Kevin, thanks for your tips. Can you please point me a suitable page for this "For the beta, OR, p-value, et cetera, please use PLINK."? Thanks in advance ...
written 6 weeks ago by
Mahan • 70
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... Hello everyone, I used to use Haploview to analyze my GWAS results but recently I'm unable to use it because of some errors it throwing. I would like to know if there is any suitable alternative for Haploview which can help me to visualize my GWAS results and also look into SNPs by beta, OR, and p-v ...
written 7 weeks ago by
Mahan • 70
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... I think your 1st point is correct, secondly, the IV (SNP or GRS) should only affect the outcome through the exposure (not independent of exposure -> outcome pathway). For your 3rd point, I have seen some papers the authors check if the SNPs they choose are also associated with potential confounde ...
written 8 weeks ago by
Mahan • 70
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... Hi Shicheng,
There are three core assumptions for MR (24–26):
1. The genetic variant is associated with the exposure
**2. The genetic variant is independent of the outcome given the exposure and all confounders (measured and unmeasured) of the exposure-outcome association**
3. The genetic varia ...
written 8 weeks ago by
Mahan • 70
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... Thanks for your advice RamRS. Let me look into that. ...
written 10 weeks ago by
Mahan • 70
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... Hi, RamRS ~ Thanks for your suggestion. Do you mind sharing the detailed steps and R code? ...
written 10 weeks ago by
Mahan • 70
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... I have: CHR START END Effect_Allele Ref_Allele columns (hg38)
I want: CHR START END Effect_Allele Ref_Allele RS_ID
I would like to get the SNP rs id using chromosome coordinates, please let me know how I can do this?
Thanks in Advance ...
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Comment:
A: QC after imputation
... Hi Aurina, I'm also in a similar situation where I have received the imputed data (from IMPUTE) in the plink format (.bed, .bim, and .fam) for ch1 to ch22 individually.
Can you please suggest me a suitable protocol/tool to perform the post imputation QC and association analysis.
Thanks in advanc ...
written 4 months ago by
Mahan • 70
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Comment:
A: How To Analyze Imputed Gwas Data
... Hello everyone
I have received the imputed data (from IMPUTE) divided into ch 1 to 22 (.bid, .bim, and .fam) files.
In the next step, I would like to perform the post imputation QC and association analysis.
I have experience working with a single file system earlier, but this is the first time ...
written 4 months ago by
Mahan • 70
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