## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE---------------- ## For links library("BiocStyle") ## Track time spent on making the vignette startTime <- Sys.time() ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation("BiocStyle")[1], GenomeInfoDb = RefManageR::BibEntry( bibtype = "manual", key = "GenomeInfoDb", author = "Sonali Arora and Martin Morgan and Marc Carlson and H. Pagès", title = "GenomeInfoDb: Utilities for manipulating chromosome and other 'seqname' identifiers", year = 2017, doi = "10.18129/B9.bioc.GenomeInfoDb" ), knitr = citation("knitr")[3], GenomicState = citation("GenomicState")[1], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], rtracklayer = citation("rtracklayer")[1], sessioninfo = citation("sessioninfo")[1], testthat = citation("testthat")[1], GenomicFeatures = citation("GenomicFeatures")[1], bumphunter = citation("bumphunter")[1], derfinder = citation("derfinder")[1], AnnotationDbi = citation("AnnotationDbi")[1], IRanges = citation("IRanges")[1], org.Hs.eg.db = citation("org.Hs.eg.db")[1], glue = citation("glue")[1], AnnotationHub = citation("AnnotationHub")[1], AnnotationHubData = citation("AnnotationHubData")[1], GenomicRanges = citation("GenomicRanges")[1], txdbmaker = citation("txdbmaker")[1] ) ## ----'install', eval = FALSE-------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("GenomicState") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----'citation'--------------------------------------------------------------- ## Citation info citation("GenomicState") ## ----setup, message = FALSE, warning = FALSE---------------------------------- library("GenomicState") ## ----'annotation_hub'--------------------------------------------------------- ## Query AnnotationHub for the GenomicState object for Gencode v31 on ## hg19 coordinates hub_query_gs_gencode_v31_hg19 <- GenomicStateHub( version = "31", genome = "hg19", filetype = "GenomicState" ) hub_query_gs_gencode_v31_hg19 ## Check the metadata mcols(hub_query_gs_gencode_v31_hg19) ## Access the file through AnnotationHub if (length(hub_query_gs_gencode_v31_hg19) == 1) { hub_gs_gencode_v31_hg19 <- hub_query_gs_gencode_v31_hg19[[1]] hub_gs_gencode_v31_hg19 } ## ----'build_ex_objects'------------------------------------------------------- ## Load the example TxDb object ## or start from scratch with: ## txdb_v31_hg19_chr21 <- gencode_txdb(version = '31', genome = 'hg19', ## chrs = 'chr21') txdb_v31_hg19_chr21 <- AnnotationDbi::loadDb( system.file("extdata", "txdb_v31_hg19_chr21.sqlite", package = "GenomicState" ) ) ## Build the GenomicState and annotated genes genes_v31_hg19_chr21 <- gencode_annotated_genes(txdb_v31_hg19_chr21) gs_v31_hg19_chr21 <- gencode_genomic_state(txdb_v31_hg19_chr21) ## ----'obtain_annotation_hub'-------------------------------------------------- ## Create the AnnotationHub object once and re-use it to speed up things ah <- AnnotationHub::AnnotationHub() ## Find the TxDb object for hg19 Gencode version 31 hub_query_txdb_gencode_v31_hg19 <- GenomicStateHub( version = "31", genome = "hg19", filetype = "TxDb", ah = ah ) hub_query_txdb_gencode_v31_hg19 ## Now the Annotated Genes for hg19 Gencode v31 hub_query_genes_gencode_v31_hg19 <- GenomicStateHub( version = "31", genome = "hg19", filetype = "AnnotatedGenes", ah = ah ) hub_query_genes_gencode_v31_hg19 ## And finally the GenomicState for hg19 Gencode v31 hub_query_gs_gencode_v31_hg19 <- GenomicStateHub( version = "31", genome = "hg19", filetype = "GenomicState", ah = ah ) hub_query_gs_gencode_v31_hg19 ## If you want to access the files use the double bracket AnnotationHub syntax ## to retrieve the R objects from the web. if (FALSE) { hub_txdb_gencode_v31_hg19 <- hub_query_txdb_gencode_v31_hg19[[1]] hub_genes_gencode_v31_hg19 <- hub_query_genes_gencode_v31_hg19[[1]] hub_gs_gencode_v31_hg19 <- hub_query_gs_gencode_v31_hg19[[1]] } ## ----'load_derfinder', messages = FALSE, warnings = FALSE--------------------- ## Load external packages library("derfinder") library("derfinderPlot") library("bumphunter") library("GenomicRanges") ## ----'example_plot_prep'------------------------------------------------------ ## Some example regions from derfinder (set the chromosome lengths) regions <- genomeRegions$regions[1:2] seqlengths(regions) <- seqlengths(txdb_v31_hg19_chr21)[ names(seqlengths(regions)) ] ## Annotate them nearestAnnotation <- matchGenes(x = regions, subject = genes_v31_hg19_chr21) annotatedRegions <- annotateRegions( regions = regions, genomicState = gs_v31_hg19_chr21$fullGenome, minoverlap = 1 ) ## Obtain fullCov object fullCov <- list("chr21" = genomeDataRaw$coverage) regionCov <- getRegionCoverage(fullCov = fullCov, regions = regions) ## ----'example_plot'----------------------------------------------------------- ## now make the plot plotRegionCoverage( regions = regions, regionCoverage = regionCov, groupInfo = genomeInfo$pop, nearestAnnotation = nearestAnnotation, annotatedRegions = annotatedRegions, whichRegions = 1:2, txdb = txdb_v31_hg19_chr21, verbose = FALSE ) ## ----'local_metadata'--------------------------------------------------------- ## Get the local metadata meta <- local_metadata() ## Subset to the data of interest, lets say hg19 TxDb for v31 interest <- subset(meta, RDataClass == "TxDb" & Tags == "Gencode:v31:hg19") ## Next you can load the data if (file.exists(interest$RDataPath)) { ## This only works at JHPCE eval(parse(text = interest$loadCode)) ## Explore the loaded object (would be gencode_v31_hg19_txdb in this case) gencode_v31_hg19_txdb } ## ----'build_local', eval = FALSE---------------------------------------------- # outdir <- "gencode" # dir.create(outdir, showWarnings = FALSE) # # ## Build and save the TxDb object # gencode_v23_hg19_txdb <- gencode_txdb("23", "hg19") # saveDb(gencode_v23_hg19_txdb, # file = file.path(outdir, "gencode_v23_hg19_txdb.sqlite") # ) # # ## Build and save the annotateTranscripts output # gencode_v23_hg19_annotated_genes <- gencode_annotated_genes( # gencode_v23_hg19_txdb # ) # save(gencode_v23_hg19_annotated_genes, # file = file.path(outdir, "gencode_v23_hg19_annotated_genes.rda") # ) # # ## Build and save the GenomicState # gencode_v23_hg19_GenomicState <- gencode_genomic_state( # gencode_v23_hg19_txdb # ) # save(gencode_v23_hg19_GenomicState, # file = file.path(outdir, "gencode_v23_hg19_GenomicState.rda") # ) ## ----'build_source'----------------------------------------------------------- ## R commands for building the files: system.file("scripts", "make-data_gencode_human.R", package = "GenomicState" ) ## The above file was created by this one: system.file("scripts", "generate_make_data_gencode_human.R", package = "GenomicState" ) ## ----createVignette, eval=FALSE----------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("GenomicState.Rmd")) # # ## Extract the R code # library("knitr") # knit("GenomicState.Rmd", tangle = TRUE) ## ----reproduce1, echo=FALSE--------------------------------------------------- ## Date the vignette was generated Sys.time() ## ----reproduce2, echo=FALSE--------------------------------------------------- ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits = 3) ## ----reproduce3, echo=FALSE------------------------------------------------------------------------------------------- ## Session info library("sessioninfo") options(width = 120) session_info() ## ----vignetteBiblio, results = 'asis', echo = FALSE, warning = FALSE, message = FALSE--------------------------------- ## Print bibliography PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))