rvtests icon indicating copy to clipboard operation
rvtests copied to clipboard

Published 20 hours ago • verified publisher icon zhanxw

Optimized SKAT (SKAT-O)

Open gpcr opened this issue 8 years ago • 5 comments

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

gpcr avatar Jul 17 '15 07:07 gpcr

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

zhanxw avatar Jul 21 '15 20:07 zhanxw

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

gpcr avatar Sep 21 '15 13:09 gpcr

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.

zhanxw avatar Dec 02 '15 05:12 zhanxw

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

gpcr avatar Dec 02 '15 13:12 gpcr

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!

7methylg avatar May 05 '17 19:05 7methylg