Description Usage Arguments Details Author(s) References Examples
To identify differentially methylated regions using a modified comb-p method
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data |
A data frame with colname name "chr","start", "end","p" and "probe", indicating chromosome (1,2,3,...,X,Y), chromosome start and end position, P value and probe names |
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 |
If TRUE, regional plots will be generated |
mht_plot |
If TRUE, mahattan plot will be generated |
nCores |
Number of computer cores will be used in calculation |
verbose |
If TRUE, detailed running information will be printed |
The input should be a data frame with column names "chr","start", "end","p", and "probe", indicating chromosome number, start position, end position, P value and probe name. The function 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, Bioinformatics 2020
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