README
¶
Module name: organelle-isolation
Calculates how isolated an NMF compartment is, i.e. for genes localizing to the compartment the number of edges between members of the compartment relative to the number of edges to proteins outside the compartment.
| parameters | definition | default |
|---|---|---|
| abundanceCap | value cap on absolute heatmap | 1000 |
| basisMatrix | NMF basis matrix | |
| correlationCutoff | cutoff to consider an interaction pair | 0.9 |
| nmfLocalization | Text file with assigned NMF rank and score for each gene | |
| nmfSummary | NMF rank summary file | |
| outFile | output file name | organelle-isolation.txt |
| svgFile | output file name for heatmap | organelle-isolation.svg |
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
nmfLocalization
gene rank score
AAAS 13 0.3326865
AAK1 5 0.1396383
AAR2 19 0.034698
AARS2 6 0.2251458
AASDH 2 0.09391108
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
organelle-isolation.txt: for each compartment lists the number of edges within the compartment and outside
heatmap: heatmap showing the absolute or relative number of edges shared between each compartments
Documentation
Source Files
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