README
¶
Module name: network-correlation
Calculate correlation between matrix rows and output Cytoscape formatted file for viewing network.
| parameters | definition | default |
|---|---|---|
| colorList | text file with hex colors | |
| cutoff | correlation cutoff to define edges | 0 |
| edgesPerNode | ideal edge number between nodes when not setting a cutoff | 20 |
| localizations | ordered list of all possible localizations | |
| maxEdges | maximum number of edges to allow per node when specifying a cutoff | 0 |
| nodeLocalizations | list of primary localizations for genes | |
| nodeProfiles | localization profiles (matrix) | |
| outFile | output file with all node pairs and edge weight (correlation) | corr.txt |
| outFileNetwork | output file name Cytoscape network | corr.cyjs |
If cutoff is > 0, it will be used to define edges, otherwise a cutoff will be sought
to achieve edgesPerNode.
Example file formats
colorList
#C0B9B2
#1CE6FF
#FF4A46
#008941
localization
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005730 nucleolus
GO:0005741 mitochondrial outer membrane
GO:0005743 mitochondrial inner membrane
nodeLocalizations
gene GO:0005694 GO:0016604 GO:0005635
AAAS 0.0000 0.0000 0.2500
AAK1 0.0000 0.2200 0.6700
Output
corr.cyjs: Cytoscape formatted file with nodes placed on a gridcorr.txt: node pairs
Documentation
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