PROMISE-package {PROMISE} | R Documentation |
a tool to identify genomic geatures with a specific biologically interesting pattern of associations with multiple endpoint variables
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.
Stan Pounds stanley.pounds@stjude.org; Xueyuan Cao xueyuan.cao@stjude.org
Maintainer: Stan Pound stanley.pounds@stjude.org; Xueyuan Cao xueyuan.cao@stjude.org
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
## 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)