sleipnir / tools / NetworkRanker / NetworkRanker.ggo

package	"NetworkRanker"
version	"1.0"
purpose	"Ranks networks for each gene based on a network connectivity score of the gene"

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  "annot" a   "matrix of gene to network annotations"
                        string typestr="filename"
option  "genesets" s   "PCL file of genesets"
                        string typestr="filename"
option  "gene" x   "Calculate gene by geneset scores"
						flag    off	
option  "geneset_idx" n   "Index of geneset when outputting by genes"
						int default="0"	

section "Compendium correction"
option "backg"     b   "Divide by background network compendium score"
						flag    on	
option "refnet" r   "Use reference network for background correction"
						string	typestr="filename"
section "Network correction"
option	"enorm"		e	"Correct by the degrees of both genes incident to an edge"
						flag	off
option	"gnorm"		g	"Correct by the degree of gene of interest"
						flag	off
option	"nnorm"		G	"Correct by the degree of neighbor gene"
						flag	off
section "Weight"
option	"log_weight"		l	"Weight by log of ratio"
						flag	off
option	"weight"		w	"Weight edges by chosen metric"
						flag	off