File Formats - Revision history

Smith: /* "Network alternative 5-column file format" */

2015-07-09T22:29:06Z

‎"Network alternative 5-column file format"

2015-07-09T22:28:43Z

‎"Network alternative 5-column file format"

2015-07-09T22:27:55Z

‎"Lab Format"

2015-02-11T21:30:21Z

‎Marker Set File Format

2015-02-11T21:30:00Z

‎Array Set File Format

2015-02-11T21:29:19Z

‎Array Set File Format

2015-02-11T21:27:02Z

‎Array Set File Format

2015-02-11T21:26:30Z

‎Pattern Discovery Export Format

2014-06-02T20:20:46Z

‎"Lab Format"

2014-06-02T20:18:26Z

‎"Lab Format"

@@ Line 208: / Line 208: @@
 	3320	0	1	0
-==="Network alternative 5-column file format"===
+===Network alternative "5-column file format"===
 Each line represents a network edge and comprises five tab-delimited columns:

← Older revision		Revision as of 22:28, 9 July 2015
Line 209:		Line 209:

	==="Network alternative 5-column file format"===		==="Network alternative 5-column file format"===
−
−	MARINa in geWorkbench will normally be set up to work with a network that is either already in the Workspace, or that is loaded from disk in a standard format, e.g. an ARACNe-style adjacency matrix or SIF file. geWorkbench will generate a file in the following 5-column format which is then sent to the remote MARINa service. However, a file in this format can also be directly loaded into the MARINa component. In this case, the values contained in the file are used directly, and are not replaced by values calculated by geWorkbench.

	Each line represents a network edge and comprises five tab-delimited columns:		Each line represents a network edge and comprises five tab-delimited columns:

@@ Line 207: / Line 207: @@
 	3320	1	0	1
 	3320	0	1	0
 ==Misc. Formats==

@@ Line 277: / Line 277: @@
 ===Marker Set File Format===
-Marker sets can be loaded from disk into the [[Markers]] component.
+Marker sets can be loaded from disk into the [[Marker_Sets|Markers]] component.
 See [[Marker_Sets#Load_Set| Marker Sets: Load Set]]
 * The file has a single column containing either probeset names or gene names.

@@ Line 268: / Line 268: @@
 ===Array Set File Format===
-Array sets can be loaded from disk into the [[Arrays]] component.
+Array sets can be loaded from disk into the [[Array_Sets|Arrays]] component.
 See [[Array_Sets#Load_Set| Array Sets: Load Set]]

@@ Line 270: / Line 270: @@
 Array sets can be loaded from disk into the Arrays component.
-See [[Array_Sets#Load_Set]]
+See [[Array_Sets#Load_Set| Array Sets: Load Set]]
 The file can contain one or two columns.
 # The first column contains array names corresponding to those in the current expression data set.
 # The optional second column can contain set names.  Each array will be assigned to the indicated set on read-in.  If a set does not already exist, it will be created.

← Older revision		Revision as of 21:26, 11 February 2015
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	[4] KKP.AKKA [3,3,7,11.941700055286251] [1,228][2,228][4,165]		[4] KKP.AKKA [3,3,7,11.941700055286251] [1,228][2,228][4,165]
	[5] AA.KKA.AAA [3,3,8,54.52686758911383] [1,193][2,194][3,61]		[5] AA.KKA.AAA [3,3,8,54.52686758911383] [1,193][2,194][3,61]
		+
		+	===Array Set File Format===
		+	Array sets can be loaded from disk into the Arrays component.
		+
		+	See [[Array_Sets#Load_Set]]
		+
		+	The file can contain one or two columns.
		+	# The first column contains array names corresponding to those in the current expression data set.
		+	# The optional second column can contain set names. Each array will be assigned to the indicated set on read-in. If a set does not already exist, it will be created.

@@ Line 198: / Line 198: @@
 * '''ppi''' - boolean: 1 if interaction is protein-protein, 0 otherwise
 * '''Dir''' - boolean: 1 if interaction is directed, 0 otherwise
 ==Misc. Formats==

@@ Line 192: / Line 192: @@
 ==="Lab Format"===
-Some tools can import networks in "Lab Format".  This format is a five column, tab-delimited file with the following column headers:
+Some tools can import networks in "Lab Format".  This format is a five column, tab-delimited file with the following column headers and content types:
-* Gene1	- identifier for gene 1
+* '''Gene1	'''- identifier for gene 1
-* Gene2	- identifier for gene 2
+* '''Gene2	'''- identifier for gene 2
-* pdi - boolean: 1 if interaction is protein-DNA, 0 otherwise
+* '''pdi''' - boolean: 1 if interaction is protein-DNA, 0 otherwise
-* ppi - boolean: 1 if interaction is protein-protein, 0 otherwise
+* '''ppi''' - boolean: 1 if interaction is protein-protein, 0 otherwise
-* Dir - boolean: 1 if interaction is directed, 0 otherwise
+* '''Dir''' - boolean: 1 if interaction is directed, 0 otherwise
 ==Misc. Formats==