radmerge - Merge CpGs to differentially methylated regions

Synopsis

$ dnmtools radmerge [OPTIONS] <radmeth-input.bed>

Description

After running radmeth followed by radadjust, it is possible to further join individually differentially methylated CpGs into differentially methylated regions. This can be achieved with the command

$ dnmtools radmerge -p 0.01 radmeth-input.bed > output-dmrs.bed

The current algorithm is conservative: it joins neighboring differentially methylated sites with p-value below 0.01 (set by the -p parameter). The output format is

chrom    start    end   dmr    num-sites   meth-diff

Above, num-sites and meth-diff are the number of significantly differentially methylated CpGs in the DMR and the estimated methylation difference, respectively. Example output might look like this:

chr1     57315   57721  dmr     10      -0.498148
chr1     58263   59009  dmr     27      -0.521182
chr1    138522  139012  dmr     13      -0.443182
chr1    149284  149444  dmr      7      -0.430453
chr1    274339  275254  dmr     18      -0.520114

Note that in addition to being conservative, the work done by radmerge is very simple, and does not consider genomic distance between neighboring sites. It will merge consecutive significant sites into one interval no matter how distant are those sites on a chromosome.

Options

 -o, -output

Output file (default: stdout).

 -p, -cutoff

P-value cutoff (default: 0.01).