to_Magellan: Create output for MAGELLAN.

Description Usage Arguments Value Note Author(s) References See Also Examples

View source: R/from_genotype_utils.R

Description

Create a fitness landscape in a format that is understood by MAGELLAN http://wwwabi.snv.jussieu.fr/public/Magellan/.

Usage

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to_Magellan(x, file,
            max_num_genotypes = 2000)

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.

Value

A file is written to disk. You can then plot and/or show summary statistics using MAGELLAN.

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

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## 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)

Bioconductor-mirror/OncoSimulR documentation built on May 31, 2017, 9:37 p.m.