combp {ENmix} | R Documentation |
To identify differentially methylated regions using a modified comb-p method
combp(data,dist.cutoff=1000,bin.size=310,seed=0.01, region_plot=TRUE,mht_plot=TRUE,nCores=10)
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 |
region_plot |
Whether to draw regional plot |
mht_plot |
Whether to draw mahattan plot |
nCores |
Number of computer cores used in calculation |
The input should be a data frame with column name V1-V5, indicating chromosome, start position, end position, P values and probe names. The function will use a modified comb-p method to identify differentially methylated regions. DMR results will be stored in a file with name "resu_combp.csv". If plot options were selected, two figure files will be generated: mht.jpg and region_plot.pdf.
Liang Niu, Zongli Xu
Pedersen BS1, Schwartz DA, Yang IV, Kechris KJ. Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. Bioinfomatics 2012
Zongli Xu, Changchun Xie, Jack A. Taylor, Liang Niu, ipDMR: Identification of differentially methyl-ated regions with interval p-values, in review