### R code from vignette source 'multiOmicsViz.Rnw' ### Encoding: UTF-8 ################################################### ### code chunk number 1: Example ################################################### 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) ################################################### ### code chunk number 2: Example ################################################### 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)