OGSA (version 1.2.0)

outMap: 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')