get-methods: Get methods for 'Gsri' class

In GSRI: Gene Set Regulation Index

Description

Access and extract results from an object of class Gsri.

Usage

getGsri(object, index, ...)
getCdf(object, index, ...)
getParms(object, ...)

Arguments

object	An object of class Gsri whose results to access.
index	Optional argument used to subset the results of individual gene sets. For details, see the plot method.
...	Additional arguments, currently not used.

Details

getGsri returns a data frame with the results of the GSRI analysis, equivalent to the display of the print and show method. For each gene set it contains the estimated fraction and total number of regulated genes, the standard deviation of the estimated fraction, the GSRI, and the total number of genes in the analysis.

getCdf returns a data frame with ECDF of the p-values for a gene set.

getParms returns a list with the parameters used in the analysis, including the weights (weight) for each gene in the gene set, the number (nBoot) of bootstraps for the calculation of the GSRI, the function (test) and its arguments (testArgs) used for assessing the differential effect between the groups, the confidence level for the GSRI, and the application of the Grenander estimatior (grenander) in the calculation of the ECDF.

Value

getGsri and getCdf return data frame with the results from the GSRI analysis and the ECDF, respectively. getParms returns a list with the parameters used in the analysis.

If more than one gene set is accessed, a list with one element per gene set is returned.

Author(s)

Julian Gehring

Maintainer: Julian Gehring <[e-mail]>

See Also

Package: GSRI-package

Class: Gsri

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

Examples

## Not run: 
getGsri(object)
getCdf(object)
getParms(object)

## End(Not run)

GSRI documentation built on Nov. 8, 2020, 7:46 p.m.