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User: curious

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curious • 470
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Posts by curious

<prev • 207 results • page 1 of 21 • next >
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You can't just liftover from one build to another using only coordinates correct?
... Lets say I have (dumb example) CHROM POS REF ALT 1 1 A T Say this site is hg19 and Ref allele is referring the forward strand and maps to position 100 on hg38. You can just blindly update the position like this correct? CHROM POS REF ALT 1 100 A ...
liftover written 12 days ago by curious • 470
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what does it mean when a plink bim file contains '*' as an allele
... I have a bim file that has lines like this `6 rs563372567 0 33966734 * G` does this just mean "not G" at a multiallelic site? Or a single nucleotide deletion perhaps (in this case deletion of G)? ...
plink written 12 days ago by curious • 470
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Comment: C: Is there a reason to limit dummy coding these alleles as 0 or 1 in this regressi
... That would make too much sense :) ...
written 6 weeks ago by curious • 470
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Is there a reason to limit dummy coding these alleles as 0 or 1 in this regression model example, instead of allowing values of 0,1,or 2?
... This is not homework its just an example I found online. They are testing association between HLA alleles and some binary disease [here][1] in the data frame they have col `DQDRa1` and `DQDRa2` for haplotypes of HLA gene DQDR. It can be 10 different alleles which they recode into a number of dumm ...
gwas logistic regression written 6 weeks ago by curious • 470
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Comment: C: What is the smallest number of cases you can have in a GWAS before interpretatio
... It was just a dummy example to illustrate the idea. I was thinking more about biobanking where you cant just pay for more cases ...
written 8 weeks ago by curious • 470
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Comment: C: logistic regression using HLA alllelic data
... To expand on this, how would it look if you did have covariate (sex). For example say I have a multialleleic locus with three possible snps: data <- data.frame("snp1"=c(runif(n=150, min=0,max=2), c(runif(n=50, min=0,max=2))), "snp2"=c(runi ...
written 8 weeks ago by curious • 470
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What is the smallest number of cases you can have in a GWAS before interpretation starts becoming troublesome
... Lets say you had 100,000 samples, but were looking at some super rare diseases. At some point I would think even given the huge overall sample size that the number of cases makes interpretation hard, even if some really small p values are obtained via GWAS. is 5 cases 99,995 controls ridiculous? ...
gwas written 8 weeks ago by curious • 470
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Comment: C: Is there anyway to get a unix parallel command to write to standard output
... This seems to make no different in terms of getting this to work but thanks for taking the time ...
written 8 weeks ago by curious • 470
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Is there anyway to get a unix parallel command to write to standard output
... `parallel bcftools stats chr{}.bcf | grep "number of records:" | cut -f 4 > chr{}.txt ::: {1..22}` This does not seem to work for me, I have encountered similar issues with bcftools utilities and gotten around it by specifying my output with `-o` instead of `>` where possible, but obviously ...
unix written 8 weeks ago by curious • 470 • updated 8 weeks ago by 2nelly • 220
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Is this the correct notation for the logistic regression I am trying to describe? I am very new to statistics notation and LaTeX
... Let me know if this is off topic, I considered stack exchange, but I was worried about the domain specific content. I am performing association tests between a binary disease outcome a large set of multiallelic sites, each having *m* alleles with *Allele* representing the allelic dosage (0,1,2). I ...
association logistic regression latex written 9 weeks ago by curious • 470

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For Why would you need to specify `--keep-allele-order` and `--a2-allele` when writing a VCF with PLINK?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For bcftools selest sites with FILTER "PASS" or "."
Scholar 4 months ago, created an answer that has been accepted. For A: conda/bioconda installation of plink fails
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Popular Question 7 months ago, created a question with more than 1,000 views. For Can two Kaplan-Meier survival curves cross and still have proportional hazards?
Scholar 8 months ago, created an answer that has been accepted. For A: conda/bioconda installation of plink fails
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Scholar 11 months ago, created an answer that has been accepted. For A: conda/bioconda installation of plink fails
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics Workstation Suggestions
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Hardware requirement for RNA-seq
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