################################################### ### chunk number 1: ################################################### #line 190 "vignettes/DEGseq/inst/doc/DEGseq.Rnw" 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) ################################################### ### chunk number 2: ################################################### #line 204 "vignettes/DEGseq/inst/doc/DEGseq.Rnw" 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") ################################################### ### chunk number 3: ################################################### #line 223 "vignettes/DEGseq/inst/doc/DEGseq.Rnw" 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") ################################################### ### chunk number 4: ################################################### #line 245 "vignettes/DEGseq/inst/doc/DEGseq.Rnw" 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") ################################################### ### chunk number 5: ################################################### #line 264 "vignettes/DEGseq/inst/doc/DEGseq.Rnw" geneExpFile <- system.file("extdata", "GeneExpExample1000.txt", package="DEGseq") set.seed(100) geneExpFile1 <- geneExpFile geneExpFile2 <- geneExpFile output <- file.path(tempdir(), "samWrapperOut.txt") expCol1=c(7,9,12,15,18) expCol2=c(8,10,11,13,16) measure1=c(-1,-2,-3,-4,-5) measure2=c(1,2,3,4,5) samWrapper(geneExpFile1=geneExpFile1, geneCol1=1, expCol1=expCol1, measure1=measure1, geneExpFile2=geneExpFile2, geneCol2=1, expCol2=expCol2, measure2=measure2, nperms=100, min.foldchange=2, max.qValue=1e-4, output=output, paired=TRUE) ################################################### ### chunk number 6: ################################################### #line 288 "vignettes/DEGseq/inst/doc/DEGseq.Rnw" 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) ################################################### ### chunk number 7: ################################################### #line 302 "vignettes/DEGseq/inst/doc/DEGseq.Rnw" 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) ################################################### ### chunk number 8: ################################################### #line 310 "vignettes/DEGseq/inst/doc/DEGseq.Rnw" kidneyR1L1 <- system.file("extdata", "kidneyChr21Bowtie.txt", package="DEGseq") liverR1L2 <- system.file("extdata", "liverChr21Bowtie.txt", package="DEGseq") refFlat <- system.file("extdata", "refFlatChr21.txt", package="DEGseq") kidneyR1L1_aln <- ShortRead::readAligned(dirname(kidneyR1L1), basename(kidneyR1L1), type="Bowtie") liverR1L2_aln <- ShortRead::readAligned(dirname(liverR1L2), basename(liverR1L2), type="Bowtie") alnBatch1 <- list(kidneyR1L1_aln) ## only use the data from kidneyR1L1 and liverR1L2 alnBatch2 <- list(liverR1L2_aln) outputDir <- file.path(tempdir(), "DEGseqAlnExample") DEGseq.aln(alnBatch1, alnBatch2, refFlat=refFlat, outputDir=outputDir, method="MARS") cat("outputDir:", outputDir, "\n") ################################################### ### chunk number 9: ################################################### #line 323 "vignettes/DEGseq/inst/doc/DEGseq.Rnw" alnBatch <- list(kidneyR1L1_aln, liverR1L2_aln) output <- file.path(tempdir(), "kidneyChr21Bowtie.exp") exp <- getGeneExp.aln(alnBatch, refFlat=refFlat, output=output) write.table(exp[30:32,], row.names=FALSE) cat("output: ", output, "\n")