moonlighting

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 the matrix.txt file
• matrix.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

Overview

Package moonlighting scores preys localized by NMF for moonlighting in more than one compartment

Index

• func Calculate(fileOptions map[string]interface{})

Functions

func Calculate

func Calculate(fileOptions map[string]interface{})

Calculate calculates prey moonlighting scores from an NMF basis file and a dissimilarity matrix.