Gsri-class {GSRI} | R Documentation |
Gsri
Objects of the class Gsri
contain the results of the GSRI analysis.
Objects of class Gsri
are returned by the gsri
methods.
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
Analysis:
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:
signature(x="Gsri", y=ANY)
Plot the empirical density of p-values and the corresponding estimated effect.
Export to file:
signature(object="Gsri", file="character")
Get methods:
signature(object="Gsri")
signature(object="Gsri")
signature(object="Gsri")
Show:
signature(obejct="Gsri")
signature(obejct="Gsri")
Julian Gehring
Maintainer: Julian Gehring <julian.gehring@fdm.uni-freiburg.de>
Package:
GSRI-package
Class:
Gsri
Methods:
gsri
getGsri
getCdf
getParms
export
sortGsri
plot
show
summary
readCls
readGct
showClass("Gsri")