eigengenes: Retrieving eigengenes from DeconResults

Description Usage Arguments Value Author(s) See Also Examples

View source: R/accessor-methods.R

Description

This is the accessor function for retrieving the eigengenes calculated by the decon method.

Usage

1

Arguments

object

An object of class DeconResults.

pvalueCutoff

numeric value giving the p-value cutoff, below which eigegenes are returned. If NULL, then the pvalueCutoff from the DeconResults object is used.

Value

A matrix with as many rows as there are samples in object, and as many columns as there were gene sets provided to decon.

Author(s)

J.A. Hackney

See Also

DeconResults, decon

Examples

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    ## Not run: 
        library(GEOquery)
        library(hgu133plus2.db)
        
        ### Get tissue/cell specific gene sets
        deconGSC <- DeconGeneSetCollection()
        
        ### Dataset with mixed immune cell lines
        GSE11058 <- getGEO("GSE11058")[[1]]
        exprs(GSE11058) <- log2(exprs(GSE11058))
        annotation(GSE11058) <- "hgu133plus2"
        
        ### Map the identifiers to Affymetrix probe sets
        deconU133GSC <- mapIdentifiers(deconGSC, AnnotationIdentifier(),
            revmap(hgu133plus2ENTREZID))
        
        ### Run the deconvolution algorithm
        deconResults <- decon(GSE11058, ~1, deconU133GSC)
        
        ### Retrieve the results
        eigengenes <- eigengenes(deconResults, pvalueCutoff = 0.05)
    
## End(Not run)

JasonHackney/GSDecon documentation built on Dec. 2, 2018, 1:12 p.m.