to_Magellan {OncoSimulR} | R Documentation

## Create output for MAGELLAN and obtain MAGELLAN statistics.

### Description

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.

### Usage

    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)

### Arguments

`x` | One of the following: A matrix (or data frame) with g + 1 columns. Each of the first g columns contains a 1 or a 0 indicating that the gene of that column is mutated or not. Column g+ 1 contains the fitness values. This is, for instance, the output you will get from `rfitness`. A two column data frame. The second column is fitness, and the first column are genotypes, given as a character vector. For instance, a row "A, B" would mean the genotype with both A and B mutated. The output from a call to `evalAllGenotypes`. Make sure you use `order = FALSE` in that call. The output from a call to `evalAllGenotypesMut`. Make sure you use `order = FALSE`. The output from a call to `allFitnessEffects` (with no order effects in the specification). The first two are the same as the format for the `genotFitness` component in `allFitnessEffects`.
`file` | The name of the output file. If NULL, a name will be created using `tempfile`.
`max_num_genotypes` | Maximum allowed number of genotypes. For some types of input, we make a call to `evalAllGenotypes`, and use this as the maximum.
`verbose` | If TRUE provide additional information about names of intermediate files.
`use_log` | Use log fitness when computing statistics. Note that the `rfitness` function outputs what should be interpreted as log-fitness values, and thus we set this option by default to `FALSE`.
`short` | Give short output when computing statistics.
`replace_missing` | From MAGELLAN's `fl_statistics`: replace missing fitness values with 0 (otherwise check that all values are specified).

### Value

`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.

### Note

If you try to pass a fitness specification with order effects you will receive an error, since that cannot be plotted with MAGELLAN.

### Author(s)

Ramon Diaz-Uriarte

### References

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

### See Also

`allFitnessEffects`, `evalAllGenotypes`, `allFitnessEffects`, `rfitness`

### Examples

    ## 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)

[Package OncoSimulR version 3.0.0 Index]