IFNMeth

Use methylation array (EPIC) data to check if your samples have been treated with IFNβ. Currently only works on whole blood. Needs the following cpgs: cg01028142, cg24678928, cg13452062, cg08888522, cg05552874, cg06188083, cg26312951, cg26505274, cg22930808, cg06981309 and cg10549986.

How to install

If devtools is already installed.
install_github("a-xavier/IFNMeth")

Otherwise install devtools first:
install.packages("devtools")
library("devtools")

Usage

IFNMeth currently includes 2 functions:

1. Predict if the sample have been treated with IFNbeta:
   results <- isTreated(Example_Data_Matrix, threshold = -0.42)
   Where Example_Data_Matrix is a beta-value matrix from EPIC methylation arrays (normalised) and threshold is the cuttof for the methylation treatment score.
   The return value is a dataframe with the methylation treatment score and the IFNbeta treatment status
2. If you know the sample has been treated with IFNbeta, guesstimate the number of days since first treatment:
   results <- DaysFromTreatment(Example_Data_Matrix)
   The return value is a named vector with a number of days for each sample representing estimated days since first treatment.

Reference

Xavier, A., M. P. Campagna, V. Maltby, T. Kilpatrick, B. Taylor, H. Butzkueven, A.-L. Ponsonby, R. Scott, V. Jokubaitis, R. Lea & J. Lechner-Scott (2023) Interferon Beta treatment is a potent and targeted epigenetic modifier in multiple sclerosis. Frontiers in Immunology, 14.