combine.sims: Combines two SetMethodSims objects.

In CancerMutationAnalysis: Cancer mutation analysis

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)

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