SetMethodsSims-class: Class representation for depositing output from simulations.

In CancerMutationAnalysis: Cancer mutation analysis

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

CancerMutationAnalysis documentation built on Nov. 8, 2020, 6:47 p.m.