User: Silvia

gravatar for Silvia
Silvia10
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New User
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5 months, 2 weeks ago
Joined:
7 months, 2 weeks ago
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Posts by Silvia

<prev • 6 results • page 1 of 1 • next >
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Comment: C: PRS regression and covariates
... Thank you both! I have corrected for population stratification and batch effects as these might bias the PRS as you said, so now I am confident I did it right. However, I am still a bit doubtful if I need to control for variables associated with my phenotype (e.g., IQ). On the one hand, I have this ...
written 5 months ago by Silvia10
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PRS regression and covariates
... Hi all, I have a quick question. In a seminar talk by Cathryn Lewis (professor of Genetic Epidemiology and Statistics at King's College London), she said that when you run a regression using Polygenic Risk Score (PRS) as your Independent Variable (IV) predicting your phenotype of interest (Dependen ...
prs covariate regression written 5 months ago by Silvia10 • updated 5 months ago by Sam3.2k
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Comment: C: Genetic QC checks in R - packages and errors
... Thank you, I think I am overcomplicating this then! I will try to do it manually too. ...
written 7 months ago by Silvia10
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Comment: C: Genetic QC checks in R - packages and errors
... thank you, I actually managed to make it work but that script allows me to have a data frame with 4 columns whereas I got more, so I cannot use it. What scripts or software do you normally use to carry out similar checks? ...
written 7 months ago by Silvia10
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Comment: C: Genetic QC checks in R - packages and errors
... Hi Sam, thank you for your reply! Yes, I have. I noticed the "impute" issue but I installed it successfully as I came across the same code you've posted. The rgl package however gave me an error: "package or namespace load failed for ‘rgl’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = ...
written 7 months ago by Silvia10
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Genetic QC checks in R - packages and errors
... Hi all, I need to perform the following Quality Control checks: 1) allele frequency (AF>5% & <95%), 2) info >0.8, 3) remove all duplicate position SNPs & 4) multi-allelic SNPs. I am currently using R to do that but because this is not exactly my field I have got a bit stuck. For ...
software error R qc snp written 7 months ago by Silvia10

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