combine.sims {CancerMutationAnalysis} | R Documentation

## Combines two SetMethodSims objects.

### Description

This function is used to combine two `SetMethodSims` objects, which have the results from simulated datasets, provided that the values for `pass.null, perc.samples,` and `spiked.set.sizes` match up when the objects are generated with the `sim.data.p.values` function.

### Usage

    combine.sims(obj1, obj2)

### Arguments

`obj1` | Object of the class `SetMethodsSims`.
`obj2` | Object of the class `SetMethodsSims`.

### Value

An object of the class `SetMethodsSims`. See `SetMethodsSims` for more details.

### 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

`SetMethodsSims-class`, `cma.set.sim`

### Examples

    ## Not run:
    ##Note that this takes a few minutes to run:
    library(KEGG.db)
    data(ParsonsGBM08)
    data(EntrezID2Name)

    setIDs <- c("hsa00250", "hsa05213")
    set.seed(831984)
    ResultsSim <-
        sim.data.p.values(cma.alter = GeneAlterGBM,
                          cma.cov = GeneCovGBM,
                          cma.samp = GeneSampGBM,
                          GeneSets =  KEGGPATHID2EXTID[setIDs],
                          ID2name = EntrezID2Name,
                          nr.iter = 2,
                          pass.null = TRUE,
                          perc.samples = c(75, 95),
                          spiked.set.sizes = 50,
                          perm.null.method = TRUE,
                          pass.null.method = TRUE)

    ResultsSim

    combine.sims(ResultsSim, ResultsSim)

    ## End(Not run)

[Package CancerMutationAnalysis version 1.29.0 Index]