### R code from vignette source 'DEGseq.Rnw' ################################################### ### code chunk number 1: DEGseq.Rnw:189-195 ################################################### library(DEGseq) geneExpFile <- system.file("extdata", "GeneExpExample5000.txt", package="DEGseq") geneExpMatrix1 <- readGeneExp(file=geneExpFile, geneCol=1, valCol=c(7,9,12,15,18)) geneExpMatrix2 <- readGeneExp(file=geneExpFile, geneCol=1, valCol=c(8,10,11,13,16)) write.table(geneExpMatrix1[30:31,],row.names=FALSE) write.table(geneExpMatrix2[30:31,],row.names=FALSE) ################################################### ### code chunk number 2: DEGseq.Rnw:203-208 ################################################### layout(matrix(c(1,2,3,4,5,6), 3, 2, byrow=TRUE)) par(mar=c(2, 2, 2, 2)) DEGexp(geneExpMatrix1=geneExpMatrix1, geneCol1=1, expCol1=c(2,3,4,5,6), groupLabel1="kidney", geneExpMatrix2=geneExpMatrix2, geneCol2=1, expCol2=c(2,3,4,5,6), groupLabel2="liver", method="MARS") ################################################### ### code chunk number 3: DEGseq.Rnw:222-229 ################################################### layout(matrix(c(1,2,3,4,5,6), 3, 2, byrow=TRUE)) par(mar=c(2, 2, 2, 2)) DEGexp(geneExpMatrix1=geneExpMatrix1, expCol1=2, groupLabel1="kidneyR1L1", geneExpMatrix2=geneExpMatrix2, expCol2=2, groupLabel2="liverR1L2", replicateExpMatrix1=geneExpMatrix1, expColR1=3, replicateLabel1="kidneyR1L3", replicateExpMatrix2=geneExpMatrix1, expColR2=4, replicateLabel2="kidneyR1L7", method="MATR") ################################################### ### code chunk number 4: DEGseq.Rnw:244-252 ################################################### kidneyR1L1 <- system.file("extdata", "kidneyChr21.bed.txt", package="DEGseq") liverR1L2 <- system.file("extdata", "liverChr21.bed.txt", package="DEGseq") refFlat <- system.file("extdata", "refFlatChr21.txt", package="DEGseq") mapResultBatch1 <- c(kidneyR1L1) ## only use the data from kidneyR1L1 and liverR1L2 mapResultBatch2 <- c(liverR1L2) outputDir <- file.path(tempdir(), "DEGseqExample") DEGseq(mapResultBatch1, mapResultBatch2, fileFormat="bed", refFlat=refFlat, outputDir=outputDir, method="LRT") ################################################### ### code chunk number 5: DEGseq.Rnw:266-272 ################################################### kidneyR1L1 <- system.file("extdata", "kidneyChr21.bed.txt", package="DEGseq") refFlat <- system.file("extdata", "refFlatChr21.txt", package="DEGseq") mapResultBatch <- c(kidneyR1L1) output <- file.path(tempdir(), "kidneyChr21.bed.exp") exp <- getGeneExp(mapResultBatch, refFlat=refFlat, output=output) write.table(exp[30:32,], row.names=FALSE) ################################################### ### code chunk number 6: DEGseq.Rnw:280-283 ################################################### geneExpFile <- system.file("extdata", "GeneExpExample1000.txt", package="DEGseq") exp <- readGeneExp(file=geneExpFile, geneCol=1, valCol=c(7,9,12,15,18,8,10,11,13,16)) write.table(exp[30:32,], row.names=FALSE)