NetworkCombiner

NetworkCombiner can replace the DAT mode of Combiner. It is faster, but achieves this by making some important assumptions. NetworkCombiner uses the mean method of combining and assumes that all gene pairs be present in all DABs being combined. Therfore, NetworkCombiner should only be used if these assumptions are met.

Usage

Basic Usage

Create a new DAB file from a directory of existing DAB files by calculating the mean for each gene pair across all of the existing DAB files.

 NetworkCombiner -d <directory of dabs> -o <combined.dab>

Detailed Usage

package "NetworkCombiner"
version "1.0"
purpose "Network(Dat/Dab) file combination(mean) tool; Assumes fully connected network with identical gene sets. It's faster than Combiner."

section "Main"
option  "output"    o   "Output file"
                        string  typestr="filename"
option  "verbosity" v   "Message verbosity"
                        int default="5"
option  "directory"     d       "input directory (must only contain input files)"
                                                string  typestr="directory"
option  "logit"         l       "logit transform the probability edge weights"
                                                flag    off
option  "znormalize"    z   "z normalize edge weights (may not be probability values)"
                        flag    off
option  "map"       m   "Map gene index among the network dabs to combine. (Should be used when the gene intex are not identical among network dabs)"
                        flag    on
option  "weights"       w       "context weight file"
                                                string  optional typestr="filename"
option  "prior"         p       "count file directory"
                                                string  optional typestr="filename"

Flag	Default	Type	Description
-d	None	DAT/DAB Directory	Input directory (must only contain input files as DAT/DAB).
-m	on	Flag	Map gene index among the network dabs to combine (should be used when the gene indices are not identical among network dabs).
-o	None	DAB file	Output file for combined network.