PROMISE2 {CCPROMISE} | R Documentation |
PROMISE analysis of two genomic sets with multiple phenotypes.
PROMISE2 (exprSet, exprSet2, geneSet = NULL, promise.pattern, strat.var = NULL, nbperm = FALSE, max.ntail = 100, nperms = 10000, seed = 13)
exprSet |
expression set of first genomic data |
exprSet2 |
expression set of second genomic data |
geneSet |
geneSet should be NULL. |
promise.pattern |
PROMISE pattern |
strat.var |
stratum variable |
nbperm |
indicator of fast permuation using negative binomial strategy, taking two valid values: FALSE or TRUE. The default is FALSE. |
max.ntail |
number of sucess if nbperm = T. Further permutation will not be performed for gene(s) or gene set(s) which max.ntail permutated statistics are greater or equal to the observed statistics, The default is 100. |
nperms |
number of permutation, default = 10,000 |
seed |
random seed, default = 13 |
The function performs PROMISE analysis for two set genomic data with a prefined phenotypic pattern. It is intermediate function called by CCPROMISE to perform PROMISE analysis with canonical correlation
The output of the function is a list of length 2. The 2 components are as following:
generes |
individual genes' test statistics and p-values for each individual endpoint and PROMISE analysis. |
setres |
Gene set level analysis is not implemented with value NULL |
Xueyuan Cao Xueyuan.cao@stjude.org, Stanley Pounds stanley.pounds@stjude.org
## load data data(exmplESet) data(exmplMSet) data(exmplGeneSet) data(exmplPat) ## Perform canonical correlation test test<- PROMISE2(exmplESet[1:10], exmplMSet[1:10], promise.pattern=exmplPat, strat.var=NULL, nbperm=FALSE, max.ntail=10, nperms=100, seed=13)