[adegenet-forum] Missing data and glPCA

[Roman Luštrik]

When centering is turned on (default), there is some imputing happening. See code here:



https://github.com/thibautjombart/adegenet/blob/9f24e97759c13e0edb1c700ca1e406d8dffcb1fd/R/glFunctions.R#L327

https://github.com/thibautjombart/adegenet/blob/9f24e97759c13e0edb1c700ca1e406d8dffcb1fd/R/glFunctions.R#L351



HTH,

Roman




--- 

“If we have data, let’s look at data. If all we have are opinions, let’s go with mine.” -- Jim Barksdale










---- On Tue, 18 Feb 2025 17:19:57 +0100 Taylor Naaykens <taylor.naaykens at utoronto.ca> wrote ---



Hi,

 

I have search for the answer in the documentation and the forums and have come across this question a few times but never the answer. When running glPCA, how does this function handle missing data? Does it do a pairwise deletion for each
 locus where there is missing data for that individual? Or does it automatically do mean imputation? I can’t find a concrete answer one way or the other in the forums.

 

Thanks

 

 

Taylor



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