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Question: Using previously calculated PCs in GENESIS
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gravatar for Stephanie M. Gogarten
10 weeks ago by
University of Washington
Stephanie M. Gogarten570 wrote:

This question was sent by email:

I am using the GENESIS package, and I have a question regarding the usage of pcair function.

Is there a way to load previously calculated PC values onto pcair function and then use these values to predict PC values for a new set of samples. I know that pcair normally works like when you specify related and unrelated set. But since I already got the PC values from the reference set, I do not want to run everything  from scratch.

Could you please let me know if this option is available and where can I find it?
 

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Stephanie M. Gogarten570
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gravatar for Stephanie M. Gogarten
10 weeks ago by
University of Washington
Stephanie M. Gogarten570 wrote:

You can use the SNPRelate package to project relatives onto existing PCs. You would first need to represent your PCs as a snpgdsPCA object, which is a list with elements sample.id, snp.id, eigenval, and eigenvect. See the man pages for snpgdsPCA, snpgdsPCASNPLoading and snpgdsPCASampLoading for more details.

library(SNPRelate)
gds <- snpgdsOpen("myfile.gds")
pca.unrel < snpgdsPCA(gds, sample.id=unrels)
snp.load <- snpgdsPCASNPLoading(pca.unrel, gdsobj=gds)
samp.load <- snpgdsPCASampLoading(snp.load, gdsobj=gds, sample.id=rels)
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Stephanie M. Gogarten570
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