User: SGMS

gravatar for SGMS
SGMS70
Reputation:
70
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Trusted
Location:
European Union
Last seen:
23 hours ago
Joined:
5 years, 6 months ago
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Posts by SGMS

<prev • 28 results • page 1 of 3 • next >
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Replacing NA values of a column using values from another column
... Hi guys, I am trying to manipulate my dataset but I have two conditions and I haven't dealt with such an issue before. For example I have: ID T value(%) H1 sex H2 1 T1 38.1 15.2 F 14.5 1 T2 39.5 14.2 M 14.5 10 T1 34.1 N F 11.4 I ...
manipulation data R written 9 days ago by SGMS70 • updated 9 days ago by genomax91k
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Comment: C: GTEX - how to upload more than one rsIDs to get gene expression or eQTL informat
... Hello, I downloaded the latest GTEx version which included SNPs and found common SNPs of GTEx with my dataset. I then compared the effect sizes (direction of betas) of my dataset to the ones in GTEx. Hope that helps! ...
written 23 days ago by SGMS70
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Comment: C: Problem with Manhattan plot
... Thanks, I have seen it and it also helped me! ...
written 16 months ago by SGMS70
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Comment: C: Problem with Manhattan plot
... Hi lurdesdl, I was wondering whether you managed to come up with a solution to your problem above. It seems I also have a a line at different p-value thresholds e.g 10^-7, 10^-5 etc. It would be great if you could give me a hint. Thanks a lot ...
written 24 months ago by SGMS70
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Comment: C: GWAS in Plink - phenotype file format
... Thanks a lot! Exactly, it's so simple but I couldn't find a source saying that precisely. ...
written 2.0 years ago by SGMS70
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GWAS in Plink - phenotype file format
... Hi everyone, My question may be too simple for experienced PLINK users, yet I cannot find the simplest answers anywhere online. I was looking for a sample analysis in plink to see how a GWAS is actually run as I am a super new user. I have created .ped and .map files using: vcftools --vcf ...
gwas snps plink phenotype written 2.0 years ago by SGMS70 • updated 2.0 years ago by zx87549.7k
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Comment: C: How to integrate GTEx data for variant annotation to understand the tissue speci
... Brilliant, thanks so much! This is of such a great help! ...
written 2.0 years ago by SGMS70
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Comment: C: How to integrate GTEx data for variant annotation to understand the tissue speci
... Hi bioinfo89, Thank you very much for your reply. Just to make sure I got it right; I downloaded the files. The rsID look-up file has variant_id and rsID columns. So when you say "Integrated the information", you mean that you matched your rsIDs of interest with the variant_ID so you could find tha ...
written 2.0 years ago by SGMS70
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GTEX - how to upload more than one rsIDs to get gene expression or eQTL information
... Hi everyone, I am trying to see how my variants affect the host gene -or other eQTLs- to see the direction of effect basically. I looked on GTEx but I only found the option of using one SNP at a time or put a list of SNPs but that is with additional info I don't have. Does anyone know how to u ...
rsids snps gtex written 2.1 years ago by SGMS70 • updated 23 days ago by optimistsso4co310
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Comment: C: How to integrate GTEx data for variant annotation to understand the tissue speci
... Hi bioinfo89, Did you manage to find a solution? I keep looking for the exact same things but cannot find any help. Thanks a lot! ...
written 2.1 years ago by SGMS70

Latest awards to SGMS

Appreciated 8 months ago, created a post with more than 5 votes. For findOverlaps function in R
Popular Question 16 months ago, created a question with more than 1,000 views. For Extraction of SNPs from the 1000G vcf file for a set of regions
Great Question 23 months ago, created a question with more than 5,000 views. For findOverlaps function in R
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Extraction of SNPs from the 1000G vcf file for a set of regions
Popular Question 4.6 years ago, created a question with more than 1,000 views. For findOverlaps function in R
Student 4.6 years ago, asked a question with at least 3 up-votes. For findOverlaps function in R

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