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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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Optimized SKAT (SKAT-O) #2

Open gpcr opened 9 years ago

gpcr commented 9 years ago

Hi Rvtest team, Thanks for creating wonderful tool. I am wondering how to use rvtest for Optimized SKAT (SKAT-O) thanks

zhanxw commented 9 years ago

Thanks for the comment. I really want to implement it but currently I have a tight schedule...

gpcr commented 8 years ago

currently Optimized SKAT (including DEP-SKAT-O, CEP-SKAT-O and RS-SKAT-O) are very important rare variant analyses.... it will be great to have them....checking to see if you get a chance to implemented.... thanks in advance

zhanxw commented 8 years ago

The current source code supports SKAT-O (--kernel skato). I will draft a release very soon. This implementation is based on SKAT R package and Shawn Lee's SKAT-O paper (in Biostatistics). I am unfamiliar with DEP-SKAT-O, CEP-SKAT-O or RS-SKAT-O, can you please provide some references? Thanks.

gpcr commented 8 years ago

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601902/ http://www.hsph.harvard.edu/xlin/pub/CEPSKATmanu+supp.pdf http://www.hsph.harvard.edu/xlin/software.html#CEPSKAT

7methylg commented 7 years ago

Hi,

Thank you for this great software! Is it safe to assume that you implemented the defaults the same as R? R and rvtest with same data and what should be the same options differ by .5 in p-value, which seems large for "numerical instability".

Thanks in advance!