PROMISE2 {CCPROMISE} | R Documentation

## PROMISE Analysis of Two Genomic Sets

### Description

PROMISE analysis of two genomic sets with multiple phenotypes.

### Usage

    PROMISE2 (exprSet, exprSet2, geneSet = NULL, promise.pattern,
        strat.var = NULL, nbperm = FALSE, max.ntail = 100, nperms = 10000,
        seed = 13)

### Arguments

`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

### Details

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

### Value

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

### Author(s)

Xueyuan Cao Xueyuan.cao@stjude.org, Stanley Pounds stanley.pounds@stjude.org

### See Also

`CCPROMISE`

### Examples

      ## 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)

[Package CCPROMISE version 1.12.0 Index]