File Formats

#File Formats

##Pairwise Interaction
###Format
This file should contain an integer on the first line representing the number of interations. The second line should be blank. This should be followed by a tab delimited line for each one of the interactions.

The columns for the interactions should be:

Column 1: ID of parent node (incoming)
Column 2: ID of child node (outgoing)
Column 3: value (1 for positive association or -1 for negative association)
Column 4: logic (0 represents "and" 1 represents "or")

• The names of nodes can contain a-z A-Z and "_" characters.
• Make sure to use tabs and to not have any extra lines within the file.

###Example 52

Infection dcar-1 1 1
Injury dcar-1 1 1
...

##Pathway File

###Format First line of the file should contain an integer representing the number of nodes

This should be followed by a section for each of the nodes. The lines for each section should be:

Line 1: Integer representing the number of input (parent) nodes that interact with that node including the node itself
Line 2: Space separated list of the node names, the first is the name of the node the section is representing
Line 3: Space separated list of the number of states for each of the respective nodes in line 2 of the section
Line 4+: The remaining lines should contain information on the probability of the combination of nodes being in each possible state

ID	Node 1 State	Node 2 State	Probability
0	1	1	P(0)
1	1	2	P(1)
2	1	3	P(2)
3	2	1	P(3)
4	2	2	P(4)
5	2	3	P(5)
6	3	1	P(6)
7	3	2	P(7)
8	3	3	P(8)

*Where the sum from P(0) to P(8) equals 1 #### This does not seam to be correct ####

The format general principals should be used to create the final part of the section. This part contains one line for each line of the table, where only the id and probability fields, separated by a space, are placed in the file. The same approach should be used for when generating this part of each section when the number of nodes and states differ from the one in the previous table.

###Example (first section of example file) 42

2
daf-16 daf-2
3 3
9

0 0.000500
1 0.000500
2 0.999500
3 0.000500
4 0.999500
5 0.000500
6 0.999500
7 0.000500
8 0.000500
...

##Observation File ###Format The first line has an integer representing the number of observations. This should be followed by a section for each of the observations. Each section should start with an integer on the first line representing the number of nodes observed. This should be followed by a line for each nodes. These lines should be in the format "name tab state".
###Example 4
2
dbl-1 1
plc-3 1
4
nipi-3 1
hsp-3 1
dcar-1 1
fasn-1 3
2
daf-16 3
sma-3 1
3
wnk-1 1
sta-2 1
daf-4 1 ...

##Estimated Parameters
###Format
Same format as the factorgraph files.

##Posterior Probabilities
###Format This file contains two tab delimited columns.
Column 1: node name
Column 2: node probability for state ###Example (for 3 states) dbl-1 0.2500
dbl-1 0.5000
dbl-1 0.2500
plc-3 0.0001
plc-3 0.0001
plc-3 0.9998
...