2.3 years ago by
It took me a second to realize the update was a comment (so, I don't know if the original user is still having an issue). However, for the sake of discussion, I'll throw some ideas out there:
1) I would like to see consistent signal from multiple probes / sites. So, if you have a way to determine that there is a region with a consistent methylation trend at multiple nearby sites, I would use some sort of measurement for that region (although precisely what to use can vary somewhat between projects).
2) In the case of suggestion #1, you would have one value per region (rather than probe / site). However, if you are familiar with R and you have a lot of sites / probes to compare, it is possible that you may want to see if you can implement something based in C++ (to speed up the time for the separate tests).
As one possible example, you can take a look at the COHCAP code for possible ideas: https://github.com/cwarden45/COHCAP/blob/master/R/COHCAP.site.R
This includes the
fastLmPure() function in RcppArmadillo, which doesn't really involve knowing Rcpp/C++ (you just have to write some sort of wrapper in R).
Also, outside of COHCAP, it also looks like you can also use the
fastLm() function in a similar way as the
lm() function: https://stackoverflow.com/questions/33584389/difference-between-fastlm-and-fastlmpure-functions-from-rcpparmadillo
To be clear, in COHCAP, the gene expression tests are for a limited number of regions, I don't do this for comparing expression and methylation. However, if this sounds helpful, then you can get some more information about the
alt.pvalue parameter in the documentation for the COHCAP.site() and COHCAP.avg.by.island() functions: