User: Silvia

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Silvia0
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Posts by Silvia

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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 15 hours ago by Silvia0
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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 2 days ago by Silvia0
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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 3 days ago by Silvia0
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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 3 days ago by Silvia0

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