################################################### ### chunk number 1: ArrayExpressHTS eval=FALSE ################################################### ## #line 99 "vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.Rnw" ## library("ArrayExpressHTS") ## aehts <- ArrayExpressHTS("E-GEOD-16190") ################################################### ### chunk number 2: ArrayExpressHTS eval=FALSE ################################################### ## #line 144 "vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.Rnw" ## library("ArrayExpressHTS") ## aehts <- ArrayExpressHTS("E-GEOD-16190", usercloud = FALSE) ################################################### ### chunk number 3: ArrayExpressHTSFolders eval=FALSE ################################################### ## #line 158 "vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.Rnw" ## dir.create("testExperiment") ## dir.create("testExperiment/data") ################################################### ### chunk number 4: prepareReference eval=FALSE ################################################### ## #line 191 "vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.Rnw" ## ## # create directory ## # ## # Please note, tempdir() is used for automamtic test ## # execution. Select directory more appropriate and ## # suitable for keeping reference data. ## # ## referencefolder = paste(tempdir(), "/reference", sep = "") ## ## dir.create(referencefolder) ## ## # download and prepare reference ## prepareReference("Homo_sapiens", version = "GRCh37.61", type = "genome", aligner = "bowtie", location = referencefolder ) ## prepareReference("Homo_sapiens", version = "GRCh37.61", type = "transcriptome", aligner = "bowtie", location = referencefolder ) ## prepareReference("Mus_musculus", version = "current", type = "genome", location = referencefolder ) ## prepareReference("Mus_musculus", version = "current", type = "transcriptome", location = referencefolder ) ## ################################################### ### chunk number 5: prepareAnnotation eval=FALSE ################################################### ## #line 214 "vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.Rnw" ## ## # download and prepare annotation ## prepareAnnotation("Homo_sapiens", "current", location = referencefolder ) ## prepareAnnotation("Mus_musculus", "NCBIM37.61", location = referencefolder ) ################################################### ### chunk number 6: runPipeline eval=FALSE ################################################### ## #line 228 "vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.Rnw" ## ## # In ArrayExpressHTS/expdata there is testExperiment, which is ## # a very short version of E-GEOD-16190 experiment, placed there ## # for testing reasons. ## # ## # Experiment in ArrayExpress: ## # http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-16190 ## # ## # the following piece of code will take ~1.5 hours to compute ## # on local PC and ~10 minutes on R-Cloud ## # ## ## # if executed on a local PC, make sure tools are available ## # to the pipeline. Check initDefaultEnvironment help page ## # for instructions. ## # ## ## # create a temporary folder where experiment will be copied ## # computing experiment in the package folder may cause issues ## # with file permissions and therefore failures. ## # ## # ## srcfolder <- system.file("expdata", "testExperiment", package="ArrayExpressHTS"); ## ## dstfolder <- tempdir(); ## ## file.copy(srcfolder, dstfolder, recursive = TRUE); ## ## # run the pipeline ## # ## # set usercloud = FALSE if executing on local PC, ## # therefore parallel computation will be disabled ## # ## aehts = ArrayExpressHTSFastQ(accession = "testExperiment", organism = "Homo_sappiens", dir = dstfolder); ## ## # load the expression set object ## loadednames = load(paste(dstfolder, "/testExperiment/eset_notstd_rpkm.RData", sep="")); ## loadednames; ## ## get('library')(Biobase); ## ## # print out the expression values ## # ## head(assayData(eset)$exprs); ## ## # print out the experiment meta data ## experimentData(eset); ## pData(eset); ##