User: muralinmars

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muralinmars70
Reputation:
70
Status:
New User
Location:
France
Last seen:
2 years, 8 months ago
Joined:
5 years, 2 months ago
Email:
m**********@gmail.com

Posts by muralinmars

<prev • 24 results • page 1 of 3 • next >
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can a rank based inverse normal transformation of a continuous trait affect the significance/power
... Hi, I have this question from the recent analysis that I have been doing. I am meta-analysing a continous trait (say TRAIT1), that is inverse normal transformed. And one particular locus that was GW significant in an earlier effort (using log-transformed values) completely loses its significance ...
gwas written 2.8 years ago by muralinmars70
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Caclulate effect estimates and SE from Z scores
... Hi, I am using a post-gwas analysis tools to test genetic overlap between different traits based on summary level data, and it requires the effect size(beta) and SE. So for summary stats that has the Z score measures, beta and SE are estimated by using the following formula that was published in ...
gwas meta-analysis R written 2.8 years ago by muralinmars70 • updated 18 months ago by zx87548.7k
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Comment: C: Binding several large matrices by column
... Hi Pierre, This works perfect and thanks for the solution. I am running in to a similar issue as mentioned in this post. It is just that I want to match the files based on chr and bp position of different files and create the matrix. So I took the liberty of tweaking your solution and here is the sy ...
written 3.0 years ago by muralinmars70
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Selecting/estimating control SNPs from genotyping array for enrichment analysis on regulatory regions
... Hi, Will try to keep it short. I am currently running enrichment analysis on regulatory regions (chromatin marks). Using this new tool called Epigwas where it estimates the enrichment score of the GW significant variants (**testSNPs**) for chromatin marks like H3K4me3. Additionally, we can also s ...
snp sequencing written 3.2 years ago by muralinmars70 • updated 3.2 years ago by genomax75k
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shapeIt - prephasing - 1000g genetic map
... Hi all, I am using shapeit to prephase the genotypes, followed by using minimac to do the imputations (with 1000g phase1 v3 as the reference panel) Now when I phase the genotypes - I would like to use the genetic map from 1000g instead of the hapmap genetic map that is mentioned in shapeit manual. ...
gwas sequencing written 4.0 years ago by muralinmars70 • updated 3.9 years ago by Biostar ♦♦ 20
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Answer: A: Cell Line/Tissue Comparison between Fantom5 and Roadmap
... I have learnt that the roadmap and Fantom cover different aspects. Roadmap - epigenomes (primarily) and Fantom (TFs). Curious to know the objective behind comparing these two datasets. Thanks ...
written 4.0 years ago by muralinmars70
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Comment: C: number of snps in the bgen file (snptest)
... Thanks, Used qctool to get a summary_stats and know the number of SNPs. ...
written 4.1 years ago by muralinmars70 • updated 17 days ago by RamRS25k
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number of snps in the bgen file (snptest)
... Hi, Is there a way to know the number of snps in the bgen file for each of the chromosome. Thanks   ...
snp snptest written 4.1 years ago by muralinmars70 • updated 20 months ago by gavinband20
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having a study based effect estimate - from individual SNPs
... Dear all, Say I want to compare the effect estimate (along with CI) of XXX locus in cohort A and cohort B What I have is beta and SE for individual snps from that locus (for each cohort) How can I possibly do this. The final comparison will be through a forest plot (example attached) Thanks in a ...
biostatistics snp written 4.2 years ago by muralinmars70
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Answer: A: Have anyone worked with Genevar tool for eQTLs and mQTLs from sanger
... Hey I am facing the same problem...I think there is some issues with the hosting site (sanger). There are few alternatives, such GRASP2 that nicely curates all the GWAS and QTL data from published resources.. here is the link.. Although it is not easy interface have to download the data and query it ...
written 4.2 years ago by muralinmars70 • updated 19 days ago by RamRS25k

Latest awards to muralinmars

Popular Question 2.7 years ago, created a question with more than 1,000 views. For deflated lambda value but inflated qq plot
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Error: Allocate vector size in R - Running in server (not local)
Popular Question 3.9 years ago, created a question with more than 1,000 views. For extract specific population (vcf) from 1000 genomes - keep option

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