hmr-rep - Hypomethylated regions across replicates

Synopsis

$ dnmtools hmr-rep [OPTIONS] <input-1.meth> <input-2.meth> ...

Description

This program is similar to hmr, but it identifies HMRs in a set of replicate methylomes. Methylation must be provided in the counts format. This program assumes only data at CpG sites and that strands are collapsed so only the positive site appears in the file (e.g. using sym).

Options

 -o, -out

output file (default: STDOUT)

 -d, -desert

maximum distance between covered CpGs in HMR (default: 1000)

 -i, -itr

max number of iterations (default: 100)

 -v, -verbose

print more run info to STDERR while the program is running.

 -post-hypo

output file for single-CpG posterior hypomethylation probability (default: none)

 -post-meth

output file for single-CpG posteiror methylation probability (default: none)

 -P, -params-in

HMM parameter file (override training step)

 -p, -params-out

write HMM parameters to this file (default: none)

 -s, -seed

specify random seed (default: 408)