User: aldoc

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aldoc10
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Posts by aldoc

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Converting SNP array variant data to VCF
... Explanations and tools to work with Illumina's TOP/BOT coding system can be found at: https://www.illumina.com/documents/products/technotes/technote_topbot.pdf gengen.openbioinformatics.org/en/latest/tutorial/coding/ Probably you can use R's crlmm package to read the final report files you have ...
written 22 months ago by aldoc10
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Reading idat files with CRLMM: Error in quantile.default
... Hi, I'm trying to read Illumina idats with crlmm in R, and I get this error: Error in quantile.default(M, c(1, 5)/6, names = FALSE) I have found multiple posts about this issue, but none of them seems to provide a general answer: - https://support.bioconductor.org/p/86109/#96072 - https ...
R snp illumina written 22 months ago by aldoc10
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Plink MDS-plot: remove population outliers twice?
... Hi, [***The next 2 MDS-based steps were aimed at 1. removing population outliers (to keep only European-ancestry subjects) and 2. obtaining population covariates only for those European-ancestry subjects, to use them later. In short, the question is: should population outliers be ...
gwas plink snp mds written 2.5 years ago by aldoc10
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Comment: C: Polygenic risk score: before or after SNP filtering?
... Hi, Answering your questions: How are you calculating PGRS? - http://image.slidesharecdn.com/007metspalu-141006151830-conversion-gate01/95/eurobioforum2014speakermetspalu-22-638.jpg?cb=1412608844; I'm using PRSice, by the way How are you calculating HWE? How are you calculating MAF? Are you cal ...
written 2.6 years ago by aldoc10
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Comment: C: Polygenic risk score: before or after SNP filtering?
... Hi, I'm taking the results from public data (another GWAS), and trying to calculate PGRS in my datasets. My question is basically about how to run QC (MAF/HWE filtering, if any) in the datasets I have. Thanks ...
written 2.6 years ago by aldoc10
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Comment: C: PRSice polygenic score with only controls
... Thanks! I tried it with two different "random phenotype" files, and gives the same results. Just for future reference, the whole command was: R --file=PRSice_v1.25.R -q --args plink PRSice_v1.25/plink_1.9_linux_160914 base referencefile.txt target myplinkfile slower 0 sinc 0.01 supper 0.5 repo ...
written 2.6 years ago by aldoc10
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PRSice polygenic score with only controls
... Hi, I'm trying to calculate polygenic scores using PRSice; my dataset contains only controls (PLINK-coded as "-9"). When running PRSice, I get the following message: Error in if (levels(as.factor(prof$PHENO))[1] == "1" & levels(as.factor(prof$PHENO))[2] == : missing value where TR ...
prsice snp polygenic written 2.6 years ago by aldoc10 • updated 2.6 years ago by coleman_jonathan410
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fcGENE conversion error: Plink dosage to bed/bim/fam
... Hi, There are some PLINK dosage files (format=1) that I need to convert to bed/bim/fam (using best guesses of genotypes). Namely, the .dose files I have are like: SNP A1 A2 F1 I1 F2 I2 ... rsXXX A T 1.692 1.699 ... ... If I understand well (http://www.b ...
dosage fcgene plink written 2.6 years ago by aldoc10 • updated 8 months ago by bg11160

Latest awards to aldoc

Popular Question 22 months ago, created a question with more than 1,000 views. For PRSice polygenic score with only controls
Popular Question 22 months ago, created a question with more than 1,000 views. For Plink MDS-plot: remove population outliers twice?
Popular Question 22 months ago, created a question with more than 1,000 views. For fcGENE conversion error: Plink dosage to bed/bim/fam

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