PROMISE2: PROMISE Analysis of Two Genomic Sets

In xueyuancao/CCPROMISE: PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data

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 [e-mail], Stanley Pounds [e-mail]

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)   
 

xueyuancao/CCPROMISE documentation built on May 6, 2023, 8:29 a.m.