to_Magellan {OncoSimulR} | R Documentation |
Export a fitness landscape in a format that is understood by MAGELLAN http://wwwabi.snv.jussieu.fr/public/Magellan/ and obtain fitness landscape statistics from MAGELLAN.
to_Magellan(x, file, max_num_genotypes = 2000) Magellan_stats(x, max_num_genotypes = 2000, verbose = FALSE, use_log = FALSE, short = TRUE, replace_missing = FALSE)
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 |
verbose |
If TRUE provide additional information about names of intermediate files. |
use_log |
Use log fitness when computing statistics. Note that
the |
short |
Give short output when computing statistics. |
replace_missing |
From MAGELLAN's |
to_Magellan
: A file is written to disk. You can then plot and/or show summary
statistics using MAGELLAN.
Magellan_stats
: MAGELLAN's statistics for fitness
landscapes. If you use short = TRUE
a vector of statistics is
returned. If short = FALSE
, MAGELLAN returns a file with
detailed statistics that cannot be turned into a simple vector of
statistics. The returned object uses readLines
and, as a
message, you are also shown the path of the file, in case you want to
process it yourself.
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) ## Default, short output Magellan_stats(allFitnessEffects(cs)) ## Long output; since it is a > 200 lines file, ## place in an object. Name of output file is given as message statslong <- Magellan_stats(allFitnessEffects(cs), short = FALSE) ## Default, short output of two NK fitness landscapes rnk1 <- rfitness(6, K = 1, model = "NK") Magellan_stats(rnk1) rnk2 <- rfitness(6, K = 4, model = "NK") Magellan_stats(rnk2)