AttractorModuleSet-class: Class AttractorModuleSet

In attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Description

This is a class representation for storing the output of the findAttractors function.

Objects from the Class

Objects are output by the function findAttractors. Objects can also be created by using new("AttractorModuleSet", ...).

Slots

eSet:

ExpressionSet which primarily stores the expression data and the phenotype/sample data sets.

cellTypeTag:

character string of the tag which stores the group membership information for the samples. Must be a column name of the data frame pData(eset).

incidenceMatrix:

incidence matrix used as input to GSEAlm.

rankedPathways:

Data frame of significantly enriched pathways, ranked first by significance and then by size.

Methods

No methods have yet been defined with class "AttractorModuleSet" in the signature.

Note

This class is better describe in the vignette.

Author(s)

Jessica Mar [e-mail]

Examples

## Not run: 
new.attractmodule <- new("AttractorModuleSet", eSet=new("ExpressionSet"), cellTypeTag=character(1), incidenceMatrix=matrix(0), rankedPathways=data.frame())

## End(Not run)

Example output

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

attract documentation built on Nov. 8, 2020, 8:04 p.m.