Identification of differentially methylated regions (DMR)

Function adapt from the combp function() of the ENmix package

Usage

combp2(data, dist.cutoff = 1000, bin.size = 310, seed = 0.01, nCores = 10)

Arguments

data

A data frame from bed format file with colname name "V1","V2", "V3","V4","V5",V1 indicate chromosome (1,2,3,...,X,Y), V2 is chromosome position, V4 is for P value and V5 for name of CpGs.

dist.cutoff

Maximum distance in base pair to combine adjacent DMRs.

bin.size

bin size for autocorrelation calculation.

seed

FDR significance threshold for initial selection of DMR region.

nCores

Number of computer cores used in calculation

Value

Results of the DMRs analysis.

• result.fdr, table of selected AMRs. For each AMR include chromosomic position, P-value, and FDR

Details

The input should be a data frame with column name V1-V5, indicating chromosome, start position,end position, pValues and probe names. The function will use a modified comb-p method to identify differentially methylated regions.

Author

Basile Jumentier