User: alessandrotestori7

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Posts by alessandrotestori7

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Haplotype LD block without genotypes
... Hi. Is there a tool which can generate haplotype blocks (with plot, like Haploview) without genotype data? I only have a list of SNPs. Thanks! ...
gwas haplotype ld written 10 days ago by alessandrotestori7250
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Comment: C: Estimating association of SNPs to different traits
... Great suggestions! Thanks a lot, Kevin. ...
written 12 days ago by alessandrotestori7250
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Comment: C: Estimating association of SNPs to different traits
... Hi Kevin! I haven't carried out association analysis myself, I only retrieved these summary statistics (OR, beta, sample size and p-value) from publicly available datasets. If I set a p-value threshold (e.g.: 1E-5) and look for SNPs below this threshold in both datasets, I can find SNPs that are si ...
written 12 days ago by alessandrotestori7250
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Comment: C: Understanding Conditional analysis
... Hi Emma, I am also doing a conditional analysis in order to see how many independent significant SNPs are in my locus of interest. Would you advise to condition all the SNPs in the locus on the lead SNP (SNP with lowest p-value) recursively, till there is no more significant SNP left? Do you reme ...
written 17 days ago by alessandrotestori7250
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Estimating association of SNPs to different traits
... Hi. I have the GWAS summary statistics from two different traits. Is there a standard procedure to assign a unique p-value to each SNP in common evaluating its association to both traits? Please let me know; thanks. ...
gwas summary statistics pvalue written 19 days ago by alessandrotestori7250 • updated 12 days ago by Biostar ♦♦ 20
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Comment: C: GWAS - approximate odds ratio and standard error
... One thing I noticed is that in my dataset - being sample size fixed for all SNPs - SE of ln(OR) and allele frequency are well correlated, so that it is easy to approximate SE for various intervals of allele frequency. For example, all SNPs with allele frequency between 0.40 and 0.41 tend to have the ...
written 6 weeks ago by alessandrotestori7250
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Comment: C: GWAS - approximate odds ratio and standard error
... One of the authors actually states that the imputed Z-score divided by the square root of the sample size yields the effect size (beta) under the standardized scale (i.e. when both phenotype and genotype are standardized to have mean 0 and variance 1). I already contacted them through their github r ...
written 6 weeks ago by alessandrotestori7250
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Comment: C: GWAS - approximate odds ratio and standard error
... I had summary statistics containing ref allele, alt allele, MAF in cases, MAF in controls, chisq, p-value, OR, L95, U95, ln(OR), SE of ln(OR) ...
written 6 weeks ago by alessandrotestori7250
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Comment: C: GWAS - approximate odds ratio and standard error
... Thanks Kevin for your comment, I have updated my post with more information. ...
written 6 weeks ago by alessandrotestori7250
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GWAS - approximate odds ratio and standard error
... Hello! I'm using ImpG-Summary (Pasaniuc et al, 2014) to perform genotype imputation from summary statistics. However, for each imputed SNP, I only get a z-score, while odds ratio and standard error are missing. The output file has - for each SNP - six columns: name of SNP, position of SNP, Ref allel ...
gwas imputation written 6 weeks ago by alessandrotestori7250 • updated 6 weeks ago by Kevin Blighe7.3k

Latest awards to alessandrotestori7

Popular Question 8 weeks ago, created a question with more than 1,000 views. For getting germline mutations
Supporter 9 months ago, voted at least 25 times.
Scholar 20 months ago, created an answer that has been accepted. For A: Question about ensembl script
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Question about ensembl script

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