extract.sims.method {CancerMutationAnalysis} | R Documentation |
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.
extract.sims.method(object, method)
object |
Object of the class |
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 |
An object of the class SetMethodsSims
. See
SetMethodsSims
for more details.
Simina M. Boca, Giovanni Parmigiani.
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
SetMethodsSims-class
,
cma.set.sim
,
cma.set.stat
## 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)