Class Gsri

Description

Objects of the class Gsri contain the results of the GSRI analysis.

Objects from the class

Objects of class Gsri are returned by the gsri methods.

Slots

result:

Data frame containing the results of the GSRI estimation, with one row for each gene set and the columns:

pRegGenes:

Fraction of regulated genes in the gene set

pRegGenesSd:

Standard deviation of pRegGenes obtained from bootstrapping.

nRegGenes:

Total number of regulated genes in the gene set.

GSRI('alpha'%):

Gene Set Regulation Index, corresponding to the ‘alpha’% quantile of the bootstrapped distribution.

nGenes:

Total number of genes in the gene set.

cdf:

List of data frames containing the ECDF of the p-values. Each data frame covers one gene set, with the columns:

pval:

P-values obtained from the test function.

cdf:

Empirical cumulative density.

parms:

List containing the parameter values used in the analysis, with the elements:

weight:

Weights for each gene in the gene set

nBoot:

Number of bootstraps for the calculation of the GSRI

test:

Statistical test function

alpha:

Confidence level for the GSRI

grenander:

Application of the Grenander estimatior in the calculation of the ECDF

testArgs:

Optional arguments for test function

Methods

Analysis:

gsri:

signature(exprs="matrix", groups="factor", geneSet="missing")

signature(exprs="ExpressionSet", groups="factor", geneSet="missing")

signature(exprs="matrix", groups="factor", geneSet="GeneSet")

signature(exprs="ExpressionSet", groups="factor", geneSet="GeneSet")

signature(exprs="matrix", groups="factor", geneSet="GeneSetCollection")

signature(exprs="ExpressionSet", groups="factor", geneSet="GeneSetCollection")

Assess the degree of differential effect in the expression data.

Visualization:

plot:

signature(x="Gsri", y=ANY)

Plot the empirical density of p-values and the corresponding estimated effect.

Export to file:

export:

signature(object="Gsri", file="character")

Get methods:

getGsri:

signature(object="Gsri")

getCdf:

signature(object="Gsri")

getParms:

signature(object="Gsri")

Show:

show:

signature(obejct="Gsri")

summary:

signature(obejct="Gsri")

Author(s)

Julian Gehring

Maintainer: Julian Gehring <julian.gehring@fdm.uni-freiburg.de>

See Also

Package: GSRI-package

Class: Gsri

Methods: gsri getGsri getCdf getParms export sortGsri plot show summary readCls readGct

Examples

showClass("Gsri")