Module name: nmf-robustness

Evaluates how robust each rank's GO terms are based on the genes used to define it. It will first define the rank by performing a GO enrichment using at most maxGenesPerRank, and then repeat this when using 90%, 80%... of the maxGenesPerRank. For each evaluation it will calculate the RBD between the list generated for maxGenesPerRank and the fractional list.

parameters	definition	default
basisMatrix	NMF basis matrix
maxGenesPerRank	maximum number of genes to use per rank for enrichments	100
minRankValue	a prey must have an NMF value at or above this value to be used for enrichment	0.25
outFile	output file name for RBD data points	robustness.txt
outFileSummary	output file name for summary (mean, SD) statistics	summary.txt
percentiles	comma-separated string defining percentiles to test, e.g "0.9,0.8"
persistence	RBO persistence value	0.9
replicates	number of replicates to perform for each percentile	3
withinRankMax	if a prey has an NMF value within this % of max in its non-primary rank, it can be used for enrichment	0.75

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

Output

• robustness.txt: RBD data points for each rank, percentile and replicate
• summary.txt: mean and SD for each rank and percentile