plageParam-class: 'plageParam' class

In rcastelo/GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data

plageParam class

Description

S4 class for PLAGE method parameter objects.

Objects of class plageParam contain the parameters for running the PLAGE method.

Usage

plageParam(
  exprData,
  geneSets,
  assay = NA_character_,
  annotation = NULL,
  minSize = 1,
  maxSize = Inf
)

Arguments

exprData	The expression data set. Must be one of the classes supported by GsvaExprData. For a list of these classes, see its help page using help(GsvaExprData).
geneSets	The gene sets. Must be one of the classes supported by GsvaGeneSets. For a list of these classes, see its help page using help(GsvaGeneSets).
assay	Character vector of length 1. The name of the assay to use in case exprData is a multi-assay container, otherwise ignored. By default, the first assay is used.
annotation	An object of class GeneIdentifierType from package GSEABase describing the gene identifiers used as the row names of the expression data set. See GeneIdentifierType for help on available gene identifier types and how to construct them. This information can be used to map gene identifiers occurring in the gene sets. If the default value NULL is provided, an attempt will be made to extract the gene identifier type from the expression data set provided as exprData (by calling gsvaAnnotation on it). If still not successful, the NullIdentifier() will be used as the gene identifier type, gene identifier mapping will be disabled and gene identifiers used in expression data set and gene sets can only be matched directly.
minSize	Numeric vector of length 1. Minimum size of the resulting gene sets after gene identifier mapping. By default, the minimum size is 1.
maxSize	Numeric vector of length 1. Maximum size of the resulting gene sets after gene identifier mapping. By default, the maximum size is Inf.

Details

Since method PLAGE does not take any method-specific parameters, this class does not add any slots to the common slots inherited from GsvaMethodParam.

PLAGE takes a number of parameters shared with all methods implemented by package GSVA but does not take any method-specific parameters. These parameters are described in detail below.

Value

A new plageParam object.

References

Tomfohr, J. et al. Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics, 6:225, 2005. DOI

See Also

GsvaExprData, GsvaGeneSets, GsvaMethodParam, zscoreParam, ssgseaParam, gsvaParam

Examples

library(GSVA)
library(GSVAdata)

data(leukemia)
data(c2BroadSets)

## for simplicity, use only a subset of the sample data
ses <- leukemia_eset[1:1000, ]
gsc <- c2BroadSets[1:100]
pp1 <- plageParam(ses, gsc)
pp1

rcastelo/GSVA documentation built on Dec. 17, 2024, 4:51 p.m.