## ----install-0, eval=FALSE, echo=TRUE----------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("sitadela") ## ----load-0, eval=TRUE, echo=FALSE, tidy=FALSE, message=FALSE, warning=FALSE---- library(sitadela) ## ----example-1, eval=TRUE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- library(sitadela) buildDir <- file.path(tempdir(),"test_anndb") dir.create(buildDir) # The location of the custom database myDb <- file.path(buildDir,"testann.sqlite") # Since we are using Ensembl, we can also ask for a version organisms <- list(mm10=100) sources <- ifelse(.Platform$OS.type=="unix",c("ensembl","refseq"),"ensembl") # If the example is not running in a multicore system, rc is ignored addAnnotation(organisms,sources,forceDownload=FALSE,db=myDb,rc=0.5) ## Alternatively # setDbPath(myDb) # addAnnotation(organisms,sources,forceDownload=FALSE,rc=0.5) ## ----example-2, eval=TRUE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- # Load standard annotation based on gene body coordinates genes <- loadAnnotation(genome="mm10",refdb="ensembl",type="gene",db=myDb) genes # Load standard annotation based on 3' UTR coordinates utrs <- loadAnnotation(genome="mm10",refdb="ensembl",type="utr",db=myDb) utrs # Load summarized exon annotation based used with RNA-Seq analysis sumEx <- loadAnnotation(genome="mm10",refdb="ensembl",type="exon", summarized=TRUE,db=myDb) sumEx ## Load standard annotation based on gene body coordinates from RefSeq #if (.Platform$OS.type=="unix") { # refGenes <- loadAnnotation(genome="mm10",refdb="refseq",type="gene", # db=myDb) # refGenes #} ## ----example-3, eval=TRUE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- # Load standard annotation based on gene body coordinates genes <- loadAnnotation(genome="mm10",refdb="ensembl",type="gene",db=myDb, asdf=TRUE) head(genes) ## ----example-4, eval=TRUE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- gtf <- system.file(package="sitadela","extdata", "gadMor1_HE567025.gtf.gz") chrom <- system.file(package="sitadela","extdata", "gadMor1_HE567025.txt.gz") chromInfo <- read.delim(chrom,header=FALSE,row.names=1) names(chromInfo) <- "length" metadata <- list( organism="gadMor1_HE567025", source="sitadela_package", chromInfo=chromInfo ) tmpdb <- tempfile() addCustomAnnotation(gtfFile=gtf,metadata=metadata,db=tmpdb) # Try to retrieve some data g <- loadAnnotation(genome="gadMor1_HE567025",refdb="sitadela_package", type="gene",db=tmpdb) g # Delete the temporary database unlink(tmpdb) ## ----example-5, eval=TRUE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- gtf <- system.file(package="sitadela","extdata", "eboVir3_KM034562v1.gtf.gz") chrom <- system.file(package="sitadela","extdata", "eboVir3_KM034562v1.txt.gz") chromInfo <- read.delim(chrom,header=FALSE,row.names=1) names(chromInfo) <- "length" metadata <- list( organism="gadMor1_HE567025", source="sitadela_package", chromInfo=chromInfo ) tmpdb <- tempfile() addCustomAnnotation(gtfFile=gtf,metadata=metadata,db=tmpdb) # Try to retrieve some data g <- loadAnnotation(genome="gadMor1_HE567025",refdb="sitadela_package", type="gene",db=tmpdb) g # Delete the temporary database unlink(tmpdb) ## ----example-5-1, eval=FALSE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- # # Setup a temporary directory to download files etc. # customDir <- file.path(tempdir(),"test_custom") # dir.create(customDir) # # # Convert from GenePred to GTF - Unix/Linux only! # if (.Platform$OS.type == "unix" && !grepl("^darwin",R.version$os)) { # # Download data from UCSC # goldenPath="http://hgdownload.cse.ucsc.edu/goldenPath/" # # Gene annotation dump # download.file(paste0(goldenPath,"eboVir3/database/ncbiGene.txt.gz"), # file.path(customDir,"eboVir3_ncbiGene.txt.gz")) # # Chromosome information # download.file(paste0(goldenPath,"eboVir3/database/chromInfo.txt.gz"), # file.path(customDir,"eboVir3_chromInfo.txt.gz")) # # # Prepare the build # chromInfo <- read.delim(file.path(customDir,"eboVir3_chromInfo.txt.gz"), # header=FALSE) # chromInfo <- chromInfo[,1:2] # rownames(chromInfo) <- as.character(chromInfo[,1]) # chromInfo <- chromInfo[,2,drop=FALSE] # # # Coversion from genePred to GTF # genePredToGtf <- file.path(customDir,"genePredToGtf") # if (!file.exists(genePredToGtf)) { # download.file( # "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf", # genePredToGtf # ) # system(paste("chmod 775",genePredToGtf)) # } # gtfFile <- file.path(customDir,"eboVir3.gtf") # tmpName <- file.path(customDir,paste(format(Sys.time(),"%Y%m%d%H%M%S"), # "tgtf",sep=".")) # command <- paste0( # "zcat ",file.path(customDir,"eboVir3_ncbiGene.txt.gz"), # " | ","cut -f2- | ",genePredToGtf," file stdin ",tmpName, # " -source=eboVir3"," -utr && grep -vP '\t\\.\t\\.\t' ",tmpName," > ", # gtfFile # ) # system(command) # # # Build with the metadata list filled (you can also provide a version) # addCustomAnnotation( # gtfFile=gtfFile, # metadata=list( # organism="eboVir3_test", # source="ucsc_test", # chromInfo=chromInfo # ), # db=myDb # ) # # # Try to retrieve some data # eboGenes <- loadAnnotation(genome="eboVir3_test",refdb="ucsc_test", # type="gene",db=myDb) # eboGenes # } ## ----example-6, eval=TRUE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- gtfFile <- system.file(package="sitadela","extdata", "gadMor1_HE567025.gtf.gz") chromInfo <- read.delim(system.file(package="sitadela","extdata", "gadMor1_HE567025.txt.gz"),header=FALSE) # Build with the metadata list filled (you can also provide a version) addCustomAnnotation( gtfFile=gtfFile, metadata=list( organism="gadMor1_test", source="ucsc_test", chromInfo=chromInfo ), db=myDb ) # Try to retrieve some data gadGenes <- loadAnnotation(genome="gadMor1_test",refdb="ucsc_test", type="gene",db=myDb) gadGenes ## ----example-7, eval=TRUE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- gtfFile <- system.file(package="sitadela","extdata", "dasNov3_JH569334.gtf.gz") chromInfo <- read.delim(system.file(package="sitadela", "extdata","dasNov3_JH569334.txt.gz"),header=FALSE) # Build with the metadata list filled (you can also provide a version) addCustomAnnotation( gtfFile=gtfFile, metadata=list( organism="dasNov3_test", source="ensembl_test", chromInfo=chromInfo ), db=myDb ) # Try to retrieve some data dasGenes <- loadAnnotation(genome="dasNov3_test",refdb="ensembl_test", type="gene",db=myDb) dasGenes ## ----example-8, eval=FALSE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- # organisms <- list( # hg18=67, # hg19=75, # hg38=101:102, # mm9=67, # mm10=101:102, # rn5=77, # rn6=101:102, # dm3=77, # dm6=101:102, # danrer7=77, # danrer10=91, # danrer11=101:102, # pantro4=90, # pantro5=101:102, # susscr3=89, # susscr11=101:102, # equcab2=94, # equcab3=101:102 # ) # # sources <- c("ensembl","ucsc","refseq","ncbi") # # addAnnotation(organisms,sources,forceDownload=FALSE,rc=0.5) ## ----pseudo-1, eval=TRUE, echo=TRUE, message=TRUE, warning=FALSE-------------- metadata <- list( organism="ORGANISM_NAME", source="SOURCE_NAME", chromInfo="CHROM_INFO" ) ## ----si-1, eval=TRUE, echo=TRUE----------------------------------------------- sessionInfo()