extract.sims.method: Extracts the p-values or q-values from a SetMethodsSims...

In CancerMutationAnalysis: Cancer mutation analysis

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)

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