Funcaeologist

Funcaeologist evaluates the cohesiveness of a given gene set within a collection of functional relationship networks or experimental result datasets. The cohesiveness is a normalized ratio of the average in-connectivity (weight of an edge connecting two genes in the set) to out-connectivity (weight of an edge including at least one gene in the set). Gene sets with higher cohesiveness a overall more functionally related and generally behave more similarly in experimental data.

Usage

Basic Usage

 Funcaeologist -g <genes.txt> -d <contexts_dir> <contexts.txt>*

Output (to standard output) the cohesiveness score for the gene set genes.txt in each context-specific network in the directory contexts_dir, which must correspond to a gene set context contexts.txt.

Detailed Usage

package "Funcaeologist"
version "1.0"
purpose "Measures association of gene sets within a collection of networks"

section "Main"
option  "genes"         g   "Gene set to investigate"
                            string  typestr="filename"
option  "directory"     d   "DAB network file directory"
                            string  typestr="directory" default="."
                            
section "Backgrounds"
option  "input"         i   "DAT/DAB file in which backgrounds are calculated"
                            string  typestr="filename"
option  "input_within"  I   "If given, DAT/DAB file in which within edges are calculated"
                            string  typestr="filename"
option  "sizes"         s   "Text file containing set sizes to test"
                            string  typestr="filename"
option  "count"         c   "Number of random gene sets to test per size"
                            int default="100"
option  "invgauss"      e   "Compute inverse gaussian lambda instead of stdev"
                            flag    off
option  "percentile"    p   "Percentile to use for p-value cutoff"
                            double  default="0.95"
option  "singles"       S   "Process single sets rather than pairs"
                            flag    off

section "Optional"
option  "normalize"     n   "Normalize to the range [0,1]"
                            flag    off
option  "threads"       t   "Number of simultaneous threads"
                            int default="1"
option  "memmap"        m   "Memory map input"
                            flag    off
option  "random"        r   "Seed random generator"
                            int default="0"
option  "verbosity"     v   "Message verbosity"
                            int default="5"

Flag	Default	Type	Description
None	None	DAT/DAB files	Functional relationship networks or datasets in which the cohesiveness of the given gene set is evaluated.
-g	stdin	Gene text file	Gene set (one gene ID per line) to be investigated for cohesiveness in the given networks.
-d	.	Directory	Directory containing functional relationship or dataset DAT/DAB files. DAT/DAB files in this directory must have names corresponding to the contexts given on the command line (e.g. if the context file "mitotic_cell_cycle.txt" is given on the command line, "mitotic_cell_cycle.dab" must exist in the directory).
-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.