README.md
In mitra-ep/slapmeg: Pathway Testing for Longitudinal Omics

SlaPMEG

This package is designed to perform a Shared latent Process Mixed Effects analysis with Globaltest.

Here is a list of functions:\ \ slapmeg fits slapmeg for a single feature-set\ multslapmeg fits slapmeg simultaneously for several feature-sets\ pairslapmeg fits slapmeg based on a computationally efficient approach\ plotslapmeg Plots the estimated random effects within the pathway \ print.slapmeg Prints the slapmeg model and results with details\ summary.slapmeg Prints the slapmeg model and results \ simslapmeg Generates joint lingitudinal observations

For details explanations and example usage check the help files within package, but here are some tips. The data need to be in the conventional genomics format, so columns indicate variables and features, whereas rows indicate subjects and repeated measurements. The formula must be supplied as a formula object. There is a function to simulate longitudinal observations, so you can give it a try if you do not have a real dataset. It is possible to use predefined pathways such as GO, KEGG, Wikipathways, and etc. as long as they are put into a list format, you can take a look at examples of creating such lists in the "Creating the Pathlists" section of rSEA package manual. If the feature-set has more than 10 features, the slapmeg function will automatically switch to the pairslapmeg which is computationally more efficient. If you had convergance issues with smaller feature-sets, try the pairslapmeg function. * The plotslapmeg function will give an insight on the source of differential expression.