CCPROMISE-package: PRojection Onto the Most Interesting Statistical Evidence...

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

Description

a tool to indentify genes that are correlated between two set of genomic variables and are associated with a predefined pattern of associations with multiple endpoint variables.

Details

Package:	CCPROMISE
Type:	Package
Version:	0.99.3
Date:	2016-10-11
License:	GPL (>=2)
LazyLoad:	yes

The CCPROMISE (Canonical correlation with PROMISE analysis) is performed by calling function CCPROMISE. The two forms of genomic data such as gene expression and methylation are passed through minimal ExpressionSet; the gene annotation (defining relationship between a gene and the two forms of genomic data), phenotypic data and definition of R routines for calculating association statistics with individual endpoint variable are same as in PROMISE package. Please refer to PROMISE package for writing user defined routines.

Author(s)

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

Maintainer: Xueyuan Cao [e-mail]

References

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

Hotelling H. (1936). Relations between two sets of variables. Biometrika, 28, 321-327

Pounds S, Cheng C, Cao X, Crews KR, Plunkett W, Gandhi V, Rubnitz J, Ribeiro RC, Downing JR, and Lamba J (2009) PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables. Bioinformatics 25: 2013-2019

Wilks, S. S. (1935) On the independence of k sets of normally distributed statistical variables. Econometrica, 3 309-326.

Examples

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

CCPROMISE documentation built on Nov. 8, 2020, 4:51 p.m.