mogamun_init {MOGAMUN} | R Documentation |
initialize evolution parameters
mogamun_init( Generations = 500, PopSize = 100, MinSize = 15, MaxSize = 50, CrossoverRate = 0.8, MutationRate = 0.1, JaccardSimilarityThreshold = 30, TournamentSize = 2, Measure = "FDR", ThresholdDEG = 0.05, MaxNumberOfAttempts = 3 )
Generations |
number of generations to run (default = 500) |
PopSize |
number of subnetworks in the population (default = 100) |
MinSize |
minimum size (no. of nodes) of the subnetworks (default = 15) |
MaxSize |
maximum size (no. of nodes) of the subnetworks (default = 50) |
CrossoverRate |
rate for the crossover (default = 0.8) |
MutationRate |
rate for the mutation (default = 0.1) |
JaccardSimilarityThreshold |
subnetworks over this Jaccard similarity threshold are considered as duplicated (default = 30) |
TournamentSize |
size of the tournament (default = 2) |
Measure |
measure to calculate the nodes scores and to determine which genes are differentially expressed (possible values PValue and FDR, default = FDR) |
ThresholdDEG |
threshold to consider a gene as significantly differerentially expressed. Note: if there is a logFC available, it is also considered |logFC|>1 (default = 0.05) |
MaxNumberOfAttempts |
maximum number of attempts to find compatible parents (default = 3) |
EvolutionParameters
EvolutionParameters <- mogamun_init( Generations = 1, PopSize = 10, MinSize = 15, MaxSize = 50, CrossoverRate = 0.8, MutationRate = 0.1, JaccardSimilarityThreshold = 30, TournamentSize = 2, Measure = "FDR", ThresholdDEG = 0.05, MaxNumberOfAttempts = 3 )