outMap {OGSA} | R Documentation

## outMap

### Description

Creates PDF color map of where outliers occur coded for molecular type

### Usage

    outMap (outList, geneList, hmName = 'PatSpecMap.pdf', plotName =
    'Outliers', truncGene = FALSE, clust=FALSE)

### Arguments

`outList` | List with all outliers generated by outCallRank or outCallTib
`geneList` | Gene set to compare against
`hmName` | Name for PDF output file
`plotName` | Header for plot
`truncGene` | if TRUE, only include genes that have outlier in the plot, default is all genes in gene set
`clust` | If TRUE, clusters data and produces dendrograms

### Value

A matrix used for generating heatmap

### References

Ochs, M. F., Farrar, J. E., Considine, M., Wei, Y., Meshinchi, S., & Arceci, R. J. (n.d.). Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1-1. doi:10.1109/tcbb.2013.153

### Examples

    data(ExampleData)
    data('KEGG_BC_GS')

    # Set up Phenotype
    phenotype <- pheno
    names(phenotype) <- colnames(cnv)

    #set up datalist
    dataSet <- list(expr,meth,cnv)

    # set up values for expr-meth-cnv in that order
    tailLRL <- c('left', 'right', 'left')

    outTibLRL <- outCallTib(dataSet, phenotype=pheno,
                             names=c('Expr', 'Meth', 'CNV'), tail=tailLRL)

    # put in your pathways here
    pdgfB <- pathGS$'BIOCARTA_PDGF_PATHWAY'
    outMap(outTibLRL, pdgfB, hmName='BC_PDGF_TIB.pdf', plotName='PDGF
    Outlier T-H LRL Calls')

[Package OGSA version 1.12.0 Index]