outMap: outMap

In OGSA: Outlier Gene Set Analysis

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')

OGSA documentation built on April 28, 2020, 6:58 p.m.