SetMethodsSims-class {CancerMutationAnalysis} | R Documentation

## Class representation for depositing output from simulations.

### Description

Stores results from the `sim.data.p.values` function.

### Objects from the class

New objects can be created using calls of the form `new("SetMethodsSims", null.dist, perc.samples, spiked.set.sizes, GeneSizes, GeneSets, Coverage, EventsBySample, Mutations, Scores, results)`

### Slots

`null.dist`:

  Object of class `"character"`. Can be either "Passenger null" or "Permutation null," depending on what method is used to get the null data.

`perc.samples`:

  Object of class `"numeric"`. Vector representing the probabilities of the spiked-in gene-sets being altered in any given sample, as percentages; for example `perc.samples = c(75, 90)` means that these probabilities are `0.75` and `0.90`.

`spiked.set.sizes`:

  Object of class `"numeric"`. Vector representing the sizes, in genes, of the spiked-in gene-sets; for example, if `perc.samples = c(75, 90)` and `spiked.set.sizes = c(50, 100)`, there would be 4 spiked-in sets, one with 50 genes and probability of being altered of 0.75 in each sample, one with 50 genes and probability of being altered of 0.90 in each sample, one with 100 genes and probability of being altered of 0.75 in each sample, and one with 100 genes and probability of being altered of 0.90 in each sample.

`GeneSets`:

  Object of class `"list"`. The entries of the list correspond to gene-sets and give the genes annotated to them.

`cma.alter`:

  Object of class `"list"`. The entries of the list are objects similar to the `GeneAlter` objects and correspond to the simulation iterations.

`cma.cov`:

  Object of class `"list"`. The entries of the list are objects similar to the `GeneCov` objects and correspond to the simulation iterations.

`cma.samp`:

  Object of class `"list"`. The entries of the list are objects similar to the `GeneSamp` objects and correspond to the simulation iterations.

`Scores`:

  Object of class `"list"`. The entries of this list are the output of `cma.scores` and correspond to the simulation iterations.

`results`:

  Object of class `"list"`. The entries of this list are the output of `cma.set.stat` and correspond to the simulation iterations.

### Methods

show

  `signature(object = "SetMethodsSims")`

### Author(s)

Simina M. Boca, Giovanni Parmigiani.

### References

Boca SM, Kinzler KW, Velculescu VE, Vogelstein B, Parmigiani G. Patient-oriented gene-set analysis for cancer mutation data. Genome Biology. DOI: 10.1186/gb-2010-11-11-r112

### See Also

`GeneCov`, `GeneSamp`, `GeneAlter`, `cma.set.sim`, `cma.set.stat`, `combine.sims`, `extract.sims.method`

[Package CancerMutationAnalysis version 1.29.0 Index]