Entering edit mode
Antoni Picornell
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40
@antoni-picornell-3780
Last seen 10.2 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.