3 ms·
Yes, the author has shared the link to R package here: https://cran.r-project.org/web/packages/XICOR/index.html https://cran.r-project.org/web/packages/XICOR/i
by malshe 5y ago
Yes, the author has shared the link to R package here:
https://cran.r-project.org/web/packages/XICOR/index.html https://cran.r-project.org/web/packages/XICOR/index.html
Edit: R code from Dr. Chatterjee's Stanford page is here - https://souravchatterjee.su.domains//xi.R https://souravchatterjee.su.domains//xi.R
If you have never worked with R, the code seems clunky so I suggest checking out Python implementation on Github here:
https://github.com/czbiohub/xicor https://github.com/czbiohub/xicor
The Python library is not from the original author though. But it's easy to read the code and it works with pandas as well.
- tpaschalis 5y agoIf anyone is interested, I've also published a Go implementation [1] of the code for float64 slices. Results seem to exactly match the R and Python implementation, so there will be a second pass focusing on performance, stability and support for categorical variables. [1] https://github.com/tpaschalis/xicor-go https://github.com/tpaschalis/xicor-go
- ur-whale 5y agoThanks, the Python code is very clear and simple and makes it super easy to understand the idea without having to digest the paper.
- zmachinaz 5y agoThe current version of the python lib seems to be extremely badly written code. Or is the algo so bad ? Takes something like 21s to compute the correlation for just 10k samples.
- flyingmutant 5y agoThis issue contains simple code that is claimed to be >300x faster: https://github.com/czbiohub/xicor/issues/17 https://github.com/czbiohub/xicor/issues/17
- malshe 5y agoThanks for locating the solution. I didn’t check the Python code myself so I wasn’t sure what was going on with the slow processing