inst/doc/multiOmicsViz.R

In multiOmicsViz: Plot the effect of one omics data on other omics data along the chromosome

### R code from vignette source 'multiOmicsViz.Rnw'

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### code chunk number 1: Example
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library("multiOmicsViz")
sourceOmics <- system.file("extdata","sourceOmics.txt",package="multiOmicsViz")
sourceOmics <- read.table(sourceOmics,header=TRUE,sep="\t",stringsAsFactors=FALSE,check.names=FALSE)
	
targetOmics1 <- system.file("extdata","targetOmics.txt",package="multiOmicsViz")
targetOmics1 <- read.table(targetOmics1,header=TRUE,sep="\t",stringsAsFactors=FALSE,check.names=FALSE)
	
targetOmicsList <- list()
targetOmicsList[[1]] <- targetOmics1
	
outputfile <- paste(tempdir(),"/heatmap",sep="")
multiOmicsViz(sourceOmics,"CNA","20",targetOmicsList,"mRNA","All",0.001,outputfile)


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### code chunk number 2: Example
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library("multiOmicsViz")
matrix1 <- system.file("extdata","sourceOmics.txt",package="multiOmicsViz")
matrix1 <- read.table(matrix1,header=TRUE,sep="\t",stringsAsFactors=FALSE,check.names=FALSE)
	
matrix2 <- system.file("extdata","targetOmics.txt",package="multiOmicsViz")
matrix2 <- read.table(matrix2,header=TRUE,sep="\t",stringsAsFactors=FALSE,check.names=FALSE)
	
sig <- calculateCorForTwoMatrices(matrix1=matrix1,matrix2=matrix2,fdr=0.01)