README
¶
Module name: nmf-moonlighting
Calculates a moonlighting score for preys in an NMF basis matrix.
The primary localization must have a score >= minRankValue to be included in the analysis, and the secondary localization must also be >= minRankValue to be a valid secondary localization.
| parameters | definition | default |
|---|---|---|
| basisMatrix | NMF basis matrix | |
| dissimilarityMatrix | a binary upper triangular matrix of rank dissimilarity | |
| minRankValue | minimum NMF score for a primary rank to include a prey in the analysis | 0.15 |
| nmfSummary | NMF rank summary file | |
| outFileHeatmap | heat map of primary v secondary rank moonlighting | heatmap.svg |
| outFileMatrix | raw values from heatmap | matrix.txt |
| outFileScores | output file | moonlighting.txt |
Example file formats
basisMatrix
variable,1,2,3
AAAS,0.0,0.18373784550412228,0.0
AAK1,0.13963834317658874,0.0,0.0
AAR2,0.0,0.016517285371126216,0.034697999230769466
AARS2,0.0,0.0,0.001598769548285137
dissimilarityMatrix
1 2 3
1 0 1 1
2 0 1
3 0
nmfSummary
rank term displayname go synonyms ic
1 [cell junction] [cell junction] [GO:0030054] [] [1.166]
2 [chromosome] [chromatin] [GO:0005694] "[[chromatid, interphase chromosome, prophase chromosome]]" [1.256]
Output
heatmap.svg: heat map for thematrix.txtfilematrix.txt: matrix with the number of times a rank scoring as a primary localization (row) was detected with a rank as a secondary localization (column)moonlighting.txt: table with prey, moonlighting score, primary rank and secondary rank
Documentation
Source Files
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