findSynexprs {attract} | R Documentation

## This function finds the synexpression groups present within a core attractor pathway module.

### Description

This function takes the modules that were inferred from the GSEA step using (`findAttractors`) and finds a set of transcriptionally coherent set of genes associated with a particular core attractor pathway, i.e. the synexpression groups.

### Usage

    findSynexprs(myIDs, myDataSet, cellTypeTag, removeGenes = NULL, min.clustersize = 5, ...)

### Arguments

`myIDs` | either a single character string or `vector` of character strings denoting the KEGG or reactome IDs of the pathway modules to be analyzed. It may also be a character codevector of gene names of a pathway if defining a custom pathway.
`myDataSet` | `AttractorModuleSet` object, output of the `findAttractors` step. This could also be an `ExpressionSet` object if using a custom pathway.
`cellTypeTag` | character string of the variable name which stores the cell-lineages or experimental groups of interest for the samples in the data set (this string should be one of the column names of pData(myEset)).
`removeGenes` | `vector` of gene names that specify those genes who demonstrate little variability across the different celltypes and thus should be removed from downstream analysis.
`min.clustersize` | `integer` specifying the minimum number of genes that must be present in clusters that are inferred.
`...` | additional arguments.

### Details

This function performs a hierarichical cluster analysis of the genes in a core attractor pathway module, and uses an informativeness metric to determine the number of optimal clusters (syenxpression groups) that describe the data.

### Value

If a single KEGG or reactome ID is specified in `pwayIds`, then a `SynExpressionSet` object is returned. If a multiple KEGG or reactome IDs are specified, then an environment object is returned where the keys are labeled "pwayIDsynexprs" (e.g. for MAPK KEGGID = 04010, the key is pway04010synexprs). The value associated with each key is a `SynExpressionSet` object.

### Author(s)

Jessica Mar

### References

Mar, J., C. Wells, and J. Quackenbush, Identifying the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape. to appear, 2010.

### Examples

    data(subset.loring.eset)
    attractor.states <- findAttractors(subset.loring.eset, "celltype", annotation="illuminaHumanv1.db")
    remove.these.genes <- removeFlatGenes(subset.loring.eset, "celltype", contrasts=NULL, limma.cutoff=0.05)
    mapk.syn <- findSynexprs("04010", attractor.states, "celltype", remove.these.genes)
    top5.syn <- findSynexprs(attractor.states@rankedPathways[1:5,1], attractor.states, "celltype", removeGenes=remove.these.genes)
    vec.geneid <- c("GI_17999531-S","GI_17978503-A")
    custom.syn <- findSynexprs(vec.geneid, subset.loring.eset, "celltype", removeGenes=remove.these.genes)

[Package attract version 1.46.0 Index]