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zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
http://www.bioconductor.org/packages/SNPRelate
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The method you take to calculate PCA, IBD and IBS #26

Closed nottwy closed 6 years ago

nottwy commented 7 years ago

SNPrelate is a very fast and useful tool so I decide to learn it carefully.

But I find SNPrelate tells little about the way it calculates. Now I want to know more about the detail of PCA, IBD and IBS analysis SNPRelate does. There are lots of manuscripts telling stories about PCA, IBD and IBS but I don't know what's the way that SNPRelate takes. I want to know more about how snp data is transformed into statistic results in SNPRelate.

Can you supply these information for us?

zhengxwen commented 7 years ago

Please take a look at the help document of each SNPRelate function: http://www.bioconductor.org/packages/release/bioc/manuals/SNPRelate/man/SNPRelate.pdf There are references in each help document.

For example, snpgdsPCA:

Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006 Dec;2(12):e190.
nottwy commented 6 years ago

I don't understand what's the difference between PCA and IBS-multidimensional scaling analysis. I think they look the same. I have looked at the help document of snpgdsIBS, but I haven't found related references.