Cell-specific methylation pattern reconstruction. Currently uses an LP formulation and solver. The lemon graph library http://lemon.cs.elte.hu/trac/lemon and the glpk LP solver http://www.gnu.org/software/glpk/ are included in this repository. The ezOptionParser.hpp is also included http://ezoptionparser.sourceforge.net/

This project uses cmake for building and required at least version 2.6.

$ git clone https://github.com/hcorrada/methylFlow.git
$ cd methylFlow
$ git submodule init
$ git submodule update
$ mkdir build && cd build
$ cmake ..
$ make
$ make install

To compile with DEBUG flags use

...
$ mkdir build_devel && cd build_devel
$ cmake -DCMAKE_BUILD_TYPE=Debug ..
$ make
...

USAGE: methylFlow -i reads.tsv -o mfoutput [OPTIONS]

OPTIONS:

-chr, -Chr ARG                    chr name for tsv files, not required for sam
                                  input file

-cpgloss, -p, -P, --cpgloss       Use cpg-loss instead of region-loss.

-e, -eps, -E, --eps ARG           Regularization parameter search threshold.

-end, -End, --end ARG             Display end instructions.

-h, -help, --help, --usage        Display usage instructions.

-i, -in, --in, --input ARG        Read input file. Default:Tab-separated format:
                                  start length strand
                                  methyl(offset[M|U]
                                  substitutions(ignored))

-l, -lam, -lambda, --lambda ARG   Regularization parameter value.

-o, -out, --out, --output ARG     Output directory. Files written:
                                  components.tsv, patterns.tsv, regions.tsv

-s, -scale, -S, --scale ARG       Scale parameter value.

-sam, -SAM, --sam                 Input file is in SAM format instead of default
                                  tab-separated format.

-start, -Start, --start ARG       Display start instructions.

-v, -verbose, -V, --verbose       Verbose option.

EXAMPLES:

methylFlow -i reads.tsv -o mfoutput -l 10.0 -s 30.0 -e 0.1

##Authors

Hector Corrada Bravo hcorrada@gmail.com
Faezeh Dorri

Center for Bioinformatics and Computational Biology
University of Maryland
http://www.cbcb.umd.edu/~hcorrada