extract.sims.method {CancerMutationAnalysis} | R Documentation

## Extracts the p-values or q-values from a SetMethodsSims object for a specific method.

### Description

This function is used to obtain a single data frame with the p-values or q-values from one of the specific gene-set analysis methods, from a `SetMethodsSims` object which has the results from simulated datasets.

### Usage

    extract.sims.method(object, method)

### Arguments

`object` | Object of the class `SetMethodsSims`.
`method` | Character string giving the method used for extraction, and whether p-values or q-values are extracted. The string should be one of the column names of the data frame resulting from the `cma.set.stat` function.

### 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`, `cma.set.stat`

### 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

    extract.sims.method(ResultsSim, "p.values.perm.null")

    ## End(Not run)

[Package CancerMutationAnalysis version 1.28.0 Index]