plageParam-class: 'plageParam' class

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

plageParam class

Description

Method-specific parameters for the PLAGE method.

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

Usage

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

Arguments

exprData	The expression data. Must be one of the classes supported by GsvaExprData. Type help(GsvaExprData) to consult the available classes.
geneSets	The gene sets. Must be one of the classes supported by GsvaGeneSets.
assay	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	The name of a Bioconductor annotation package for the gene identifiers occurring in the row names of the expression data matrix. This can be used to map gene identifiers occurring in the gene sets if those are provided in a GeneSetCollection. By default gene identifiers used in expression data matrix and gene sets are matched directly.
minSize	Minimum size of the resulting gene sets after gene identifier mapping. By default, the minimum size is 1.
maxSize	Maximum size of the resulting gene sets after gene identifier mapping. By default, the maximum size is Inf.

Details

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

PLAGE does not take any method-specific parameters in addition to an expression data set and a collection of gene sets.

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 April 29, 2024, 11:26 a.m.