User: alerodriguez

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alerodriguez40
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Posts by alerodriguez

<prev • 40 results • page 1 of 4 • next >
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Comment: C: FastQTL - GNU Scientific Library (GSL) Domain Error
... Thank you very much for your comment, this makes a lot more sense now. I also agree that perhaps having all of the LD proxies is probably better since "To discover the best candidate QTL for P, FastQTL measures Pearson product-moment correlation coefficients between P and all L variants in G" but I ...
written 12 hours ago by alerodriguez40
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Answer: A: What is the best way to quantile normalize expression matrix ?
... Thank you very much for answering this question Devon, I have a follow-up question: Under what circumstances is it appropriate to do both log transformation and quantile normalization? Thank you in advance. ...
written 7 days ago by alerodriguez40
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FastQTL-Finding a candidate QTL per phenotype
... Can someone please explain in detail the meaning of the following section of the paper **2.2 Finding a candidate QTL per phenotype** For simplicity, we will focus on a single molecular phenotype P quantified in a set of N samples. Let G be the set of genotype dosages at L variant sites located withi ...
fastqtl written 16 days ago by alerodriguez40
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Answer: A: FastQTL - GNU Scientific Library (GSL) Domain Error
... Can someone please explain in detail the meaning of the following section of the paper > **2.2 Finding a candidate QTL per phenotype** For simplicity, we will focus on a single molecular phenotype P quantified in a set of N > samples. Let G be the set of genotype dosages at L variant sites &g ...
written 16 days ago by alerodriguez40 • updated 16 days ago by WouterDeCoster22k
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veqtl-mapper in a replication study --perm option
... Hi, I am trying to use veqtl-mapper in a replication study. In my original population, I found one veqtl and I am using a second population to replicate this finding using the veqtl-SNP and also its LD proxies. My question is, do I need to permute? If not how can veqtl-mapper be run with permuting, ...
permutations veqtl-mapper ld replication written 16 days ago by alerodriguez40
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Answer: A: How to solve the problem when I get error message "column 1 is not a genotype ob
... how can one create a data.frame which looks like the CEUSNP from a vcf file?. ...
written 21 days ago by alerodriguez40
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Answer: A: Readvcf In R
... I found this tutorial very useful especially for reading data into R https://adairama.wordpress.com/2013/02/15/functionally-annotate-snps-and-indels-in-bioconductor/#comment-738 ...
written 21 days ago by alerodriguez40
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Comment: C: Readvcf In R
... True but if i read my own data using readVcf: file <- readVcf("file.vcf","hg19") the commands hdr <- scanVcfHeader(file) **Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘scanVcfHeader’ for signature ‘"CollapsedVCF"’** and cannot follow the ...
written 21 days ago by alerodriguez40
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Answer: A: ld matrix in plink
... add the --noweb if you want this to be done quickly ...
written 22 days ago by alerodriguez40
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Answer: A: What Does Genetype ("0/0", "0/1" Or "1/1") In *.Vcf File Represent?
... Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7. The variant call format and VCFtools. should help. ...
written 4 weeks ago by alerodriguez40

Latest awards to alerodriguez

Supporter 21 days ago, voted at least 25 times.
Popular Question 5 months ago, created a question with more than 1,000 views. For merging two bigwig files

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