Edges2Posteriors

Edges2Posteriors calculates the individual contribution of every dataset to every gene pair in a predicted functional relationship network. This is similar to BNTruster, but the contributions are broken down per gene pair (rather than per dataset value, and the output can thus be much larger) and given as the actual difference in posterior probability incurred by each gene pair's individual data values.

Usage

Basic Usage

 Edges2Posteriors -i <predictions.dab> -n <learned.xdsl> -d <data_dir>

Output (to standard output) the contribution of each dataset DAT/DAB file in data_dir to the predicted functional relationship probabilities in predictions.dab based on the Bayesian network learned.xdsl; this network must contain node IDs corresponding to the data file names.

Detailed Usage

package "Edges2Posteriors"
version "1.0"
purpose "Calculate contribution of each dataset for a given list of edges"

section "Main"
option  "input"     i   "Prediction DAT/DAB file"
                        string  typestr="filename"  yes
option  "network"   n   "Input Bayesian network (X)DSL"
                        string  typestr="filename"
option  "directory" d   "Directory with DAB files"
                        string  typestr="directory" default="."

section "Miscellaneous"
option  "netdir"    N   "Directory with Bayesian network (X)DSL files for context average"
                        string  typestr="directory"
option  "lookup"    l   "Lookup pair set"
                        string  typestr="filename"
option  "cutoff"    c   "Use input network edges and exclude edges below cutoff"
                        double
section "Optional"
option  "memmap"    m   "Memory map input/output"
                        flag    off
option  "verbosity" v   "Message verbosity"
                        int default="5"
option  "start"     S   "Process only the starting at dataset index"
                        int default="-1"
option  "end"       E   "Process only up to this ending dataset index"
                        int default="-1"

Flag	Default	Type	Description
-i	stdin	DAT/DAB file	Input DAT/DAB file containing predicted functional relationships.
-n	None	(X)DSL file	Input Bayesian network for which posterior probabilities are to be analyzed.
-d	.	Directory	Directory from which DAT/DAB data files are read; must have file names corresponding to the input (X)DSL's node IDs and be accompanied by appropriate QUANT files agreeing with that (X)DSL's probability tables.
-Z	None	Tab-delimited text file	If given, argument must be a tab-delimited text file containing two columns, the first node IDs and the second bin numbers (zero indexed). For each node ID present in this file, missing values will be substituted with the given bin number.
-l	None	Gene pair text file	Tab-delimited text file containing one pair of gene IDs per row. If given, lookup values for all requested pairs.
-m	off	Flag	If given, memory map the input files when possible. DAT and PCL inputs cannot be memmapped.