pcaMethods and categorical NAs
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Last seen 7.1 years ago
Hello, I'm trying to impute missing values in a matrix built with genotypes. The values in this matrix are the "usual" ones in this situation: 0,1,2 for homozygous(0 and 2) or heterozygous (1) situations. Thus, I have a matrix with 0,1,2 and NAs. I want t impute these NAs. I have found that the package pcaMethods could be a nice way to impute NAs in huge ammounts of data. The other solution I have found is fastPHASE, but it is very slow. However, as far as I know pcaMethods needs a numerical matrix. Anybody knows whether this package can be applied in this situation? I have not seen anything related to this issue in the vignettes. Do you use another package to do this? Thanks, Antoni Picornell.
impute impute • 534 views

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