Funcifier

Funcifier (pronounced funk-if-eyer, not fun-siffier, with flagrant disregard for rules of standard English) calculates the strength of functional association between processes or pathways in a given functional relationship (or data) network. A functional association between two gene sets (e.g. pathways) measures the amount of cross-talk between those processes, which is calculated from the given individual gene pair functional relationships.

Usage

Basic Usage

 Funcifier -i <network.dab> -o <functions.dab> -l <colors.txt> <contexts.txt>*

Find the strength of functional association between every pair of contexts contexts.txt in the functional relationship network network.dab and store the resulting function pair network in functions.dab; if requested, output the cohesiveness score for each function in colors.txt for use with Dat2Graph.

Detailed Usage

package "Funcifier"
version "1.0"
purpose "Function interaction network builder"

section "Main"
option  "input"         i   "Input interaction network"
                            string  typestr="filename"  yes
option  "output"        o   "Output function network"
                            string  typestr="filename"  yes

section "Miscellaneous"
option  "shared"        s   "Determine shared gene handling"
                            values="ignore","discard","oneonly" default="discard"
option  "colors"        l   "Function cohesiveness output file"
                            string  typestr="filename"
option  "weights"       w   "PCL file of set-by-gene weights"
                            string  typestr="filename"
option  "minimum"       u   "Minimum edge count/weight to use"
                            double  default="0"

section "Optional"
option  "normalize"     n   "Normalize input to the range [0,1]"
                            flag    off
option  "zscore"        z   "Normalize output by z-scoring"
                            flag    off
option  "memmap"        m   "Memory map input"
                            flag    off
option  "verbosity"     v   "Message verbosity"
                            int default="5"

Flag	Default	Type	Description
None	None	Gene text files	Gene sets which will be tested for functional association in the given dataset. Each set generally represents a biological context, e.g. process or pathway. Elements in the output DAT/DAB file will be named according to these input filenames.
-i	stdin	DAT/DAB file	Input DAT/DAB file containing the functional relationship or data network to be mined for gene set functional associations.
-o	stdout	DAT/DAB file	Output DAT/DAB file containing functional associations between gene sets. While the input network contains individual gene pairs, the output network contains pairs of gene sets (e.g. each element is a pair of labels from gene sets given on the command line).
-s	discard	discard, ignore, or oneonly	Way in which genes present in multiple gene sets are handled. discard prevents shared genes from contributing to any gene set's associations, ignore allows them to contribute to every gene set in which they're included, and oneonly allows genes to contribute only if they are shared between exactly two processes (i.e. they have only one overlap).
-l	None	Text file	If given, output file into which cohesiveness scores for each gene set are placed. Output is compatible with color input for Dat2Graph.
-n	off	Flag	If on, normalize input edges to the range [0,1] before processing.
-m	off	Flag	If given, memory map the input files when possible. DAT and PCL inputs cannot be memmapped.