to_Magellan {OncoSimulR} | R Documentation |
Create a fitness landscape in a format that is understood by MAGELLAN http://wwwabi.snv.jussieu.fr/public/Magellan/.
to_Magellan(x, file, max_num_genotypes = 2000)
x |
One of the following:
The first two are the same as the format for the |
file |
The name of the output file. If NULL, a name will be
created using |
max_num_genotypes |
Maximum allowed number of genotypes. For some
types of input, we make a call to |
A file is written to disk. You can then plot and/or show summary statistics using MAGELLAN.
If you try to pass a fitness specification with order effects you will receive an error, since that cannot be plotted with MAGELLAN.
Ramon Diaz-Uriarte
MAGELLAN web site: http://wwwabi.snv.jussieu.fr/public/Magellan/
Brouillet, S. et al. (2015). MAGELLAN: a tool to explore small fitness landscapes. bioRxiv, 31583. http://doi.org/10.1101/031583
allFitnessEffects
,
evalAllGenotypes
,
allFitnessEffects
,
rfitness
## Generate random fitness for four-genes genotype ## and export landscape. r1 <- rfitness(4) to_Magellan(r1, NULL) ## Specify fitness using a DAG and export it cs <- data.frame(parent = c(rep("Root", 3), "a", "d", "c"), child = c("a", "b", "d", "e", "c", "f"), s = 0.1, sh = -0.9, typeDep = "MN") to_Magellan(allFitnessEffects(cs), NULL)