PROMISE-package: PRojection Onto the Most Interesting Statistical Evidence

In PROMISE: PRojection Onto the Most Interesting Statistical Evidence

Description

a tool to identify genomic geatures with a specific biologically interesting pattern of associations with multiple endpoint variables

Details

Package:	PROMISE
Type:	Package
Version:	1.17.0
Date:	2014-6-24
License:	GPL (>=2)
LazyLoad:	yes

The PROMISE (PRojection Onto the Most Interesting Statistical Evidence) is performed by calling function PROMISE. The array data and endpoint data are passed through an ExpressionSet; the gene set definition is passed through a GeneSetCollection, and PROMISE definition is passed through a data frame. promise.genestat and avg.abs.genestat are called internally by PROMISE. Two R routines for calculating association statistics with individual endpoint variable(jung.rstat and spearman.rstat) are provided in this version. Users could provide their own R routines written in a similar fashion.

Author(s)

Stan Pounds [e-mail]; Xueyuan Cao [e-mail]

Maintainer: Stan Pound [e-mail]; Xueyuan Cao [e-mail]

References

Jung, S-H, Owzar K, and Goerge SL (2005) A multiple testing procedure to associate gene expression levels with survival. Biostatistics 24: 3077-3088.

Goeman JJ and Buhlmann P (2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23: 980-987.

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

Examples

## load sampExprSet, sampGeneSet, phPatt.
data(sampExprSet)
data(sampGeneSet)
data(phPatt)

## Perform PROMISE procedure without GSEA
test1 <- PROMISE(exprSet=sampExprSet,
                 geneSet=NULL, 
                 promise.pattern=phPatt, 
                 strat.var=NULL,
                 proj0=FALSE,
                 nbperm=FALSE, 
                 max.ntail=10,
                 seed=13, 
                 nperms=100)
             
## Perform PROMISE procedure with GSEA and using fast permuation              
test2 <- PROMISE(exprSet=sampExprSet,
                 geneSet=sampGeneSet, 
                 promise.pattern=phPatt, 
                 strat.var=NULL,
                 proj0=TRUE,
                 nbperm=TRUE, 
                 max.ntail=10,
                 seed=13, 
                 nperms=100)

PROMISE documentation built on Nov. 8, 2020, 5:15 p.m.