CCPROMISE: PROMISE Analysis with Canonical Correlation for Two Forms of...

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

PROMISE Analysis with Canonical Correlation for Two Forms of Genomic Data

Description

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

Usage

CCPROMISE (geneSet, ESet, MSet, promise.pattern, strat.var = NULL, 
    prlbl = NULL, EMlbl = c("Expr", "Mthyl"), 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
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 CANN and PROMISE2

Value

The output is a list of length 4. The 4 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
CCres	result of canonical correlation analysis with six columns: Gene: Gene names; n.EMlbl[1]: number of probe set in the first form data; n.EMlbl[2]: number of probe set in the second form data; CanonicalCR: Canonical correlation of first components; WilksPermPval: permuatation p value of Wilks' Lambda; WilksAsymPval: p value of F-approximations of Wilks' Lambda.
FSTccscore	loads of first component of canonical correlation: a data frame of loading (each row is for a gene, first column is gene names, second column is the probeset ids of first form genomic data seperated by '|', third column is the load for each probeset in first form genomic data seperated by '|', fourth column is the probeset ids of second form genomic data seperated by '|', fifth column is the load for each probeset in second form genomic data seperated by '|')
CCload	a data frame of loading (each row is for a gene, first column is gene names, second column is the probeset ids of first form genomic data seperated by '|', third column is the load for each probeset in first form genomic data seperated by '|', fourth column is the probeset ids of second form genomic data seperated by '|', fifth column is the load for each probeset in second form genomic data seperated by '|')

Author(s)

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

References

Cao X, Crews KR, Downing J, Lamba J and Pounds SB (2016) CC-PROMISE effectively integrates two forms of molecular data with multiple biologically related endpoint. BMC Bioinformatics 17(Suppl 13):382

See Also

CANN PROMISE2

Examples

  ## load data
  data(exmplESet)
  data(exmplMSet)
  data(exmplGeneSet)
  data(exmplPat)
  ## Perform canonical correlation test
 test<- CCPROMISE(geneSet=exmplGeneSet, 
              ESet=exmplESet, 
              MSet=exmplMSet, 
              promise.pattern=exmplPat,
              strat.var=NULL,
              prlbl=NULL, 
              EMlbl=c("Expr", "Methyl"),
              nbperm=FALSE,
              max.ntail=10,
              nperms=100,
              seed=13)   
 

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