PrbPROMISE: PROMISE Analysis with Two Forms of Genomic Data at Probe...

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

PROMISE Analysis with Two Forms of Genomic Data at Probe Level

Description

PROMISE analysis of two genomic sets with multiple phenotypes under a predefined association pattern at probe level.

Usage

PrbPROMISE (geneSet, ESet, MSet, promise.pattern, strat.var = NULL, 
    prlbl = NULL, EMlbl = c("Expr", "Mthyl"), pcut = 0.05, nbperm = FALSE, 
    max.ntail = 100, nperms = 10000, seed = 13) 

Arguments

geneSet	a gene set collection to annotate probes to gene
ESet	an ExpressionSet class contains minimum of exprs (expression matrix) of first form of genomic data such as gene expression and phenoData (AnnotatedDataFrame of end point data). Please refer to Biobase for details on how to create such an ExpressionSet expression set.
MSet	an ExpressionSet class of second form of genomic data such as methylation levels, the subject id of MSet and ESet should be exactly same
promise.pattern	PROMISE pattern
strat.var	stratum variable
prlbl	labels
EMlbl	lablel of the genomic data, default=c('Expr', 'Methyl') for ESet and MSet
pcut	p value cutoff to eliminate probe pairs that are not significantly correlated. Default is 0.05
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	initial seed of random number generator. The default is 13.

Details

The function performs PROMISE analysis for two forms of genomic data in minimal expression set format with a prefined phenotypic pattern. It calls two external function PrbCor and PROMISE2

Value

The output of the function is a list of length 2. The 2 components are as following:

PRres	PROMISE result for the first component of canonical correlation between two forms of geneomic data. individual genes' test statistics and p-values for each individual endpoint and PROMISE analysis
CORres	result of spearman correlation analysis of probe pairs within a gene with five columns: Gene: Gene names; EMlbl[1]: probe id in the first form data; EMlbl[2]: probe id in the second form data; Spearman.rstat: Spearman r statistics; Spearman.p: Spearman p value.

Author(s)

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

See Also

PrbCor PROMISE2

Examples

  ## load data
  data(exmplESet)
  data(exmplMSet)
  data(exmplGeneSet)
  data(exmplPat)
  ## Perform probe level PROMISE analysis
test<-PrbPROMISE(geneSet=exmplGeneSet, 
              ESet=exmplESet, 
              MSet=exmplMSet, 
              promise.pattern=exmplPat,
              strat.var=NULL,
              prlbl=c('LC50', 'MRD22', 'EFS', 'PR3'), 
              EMlbl=c("Expr", "Methyl"),
              nbperm=TRUE,
              max.ntail=10,
              nperms=100,
              seed=13)
 

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