## ----style, echo = FALSE, results = 'asis'--------------------------------- BiocStyle::markdown() ## ---- echo=FALSE, results="hide"------------------------------------------- # Ensure that any errors cause the Vignette build to fail. library(knitr) opts_chunk$set(error=FALSE) ## ---- echo = FALSE--------------------------------------------------------- apiKey <- Sys.getenv("GOOGLE_API_KEY") if (nchar(apiKey) == 0) { warning(paste("To build this vignette, please setup the environment variable", "GOOGLE_API_KEY with the public API key from your Google", "Developer Console before loading the GoogleGenomics package,", "or run GoogleGenomics::authenticate.")) knitr::knit_exit() } ## ----message=FALSE--------------------------------------------------------- library(GoogleGenomics) # This vignette is authenticated on package load from the env variable GOOGLE_API_KEY. # When running interactively, call the authenticate method. # ?authenticate ## -------------------------------------------------------------------------- variants <- getVariants() length(variants) ## -------------------------------------------------------------------------- class(variants) mode(variants) ## -------------------------------------------------------------------------- names(variants[[1]]) ## -------------------------------------------------------------------------- length(variants[[1]]$calls) ## -------------------------------------------------------------------------- names(variants[[1]]$calls[[1]]) ## -------------------------------------------------------------------------- variants[[1]]$referenceName variants[[1]]$start variants[[1]]$alternateBases variants[[1]]$calls[[1]] ## -------------------------------------------------------------------------- variantsToVRanges(variants) ## ----message=FALSE--------------------------------------------------------- library(VariantAnnotation) ## -------------------------------------------------------------------------- granges <- getVariants(variantSetId="10473108253681171589", chromosome="22", start=50300077, end=50303000, converter=variantsToGRanges) ## ----message=FALSE--------------------------------------------------------- library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## -------------------------------------------------------------------------- txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene granges_locations <- locateVariants(granges, txdb, CodingVariants()) granges_locations ## ----message=FALSE--------------------------------------------------------- library(BSgenome.Hsapiens.UCSC.hg19) ## -------------------------------------------------------------------------- granges_coding <- predictCoding(rep(granges, elementNROWS(granges$ALT)), txdb, seqSource=Hsapiens, varAllele=unlist(granges$ALT, use.names=FALSE)) granges_coding ## ----message=FALSE--------------------------------------------------------- library(org.Hs.eg.db) ## -------------------------------------------------------------------------- annots <- select(org.Hs.eg.db, keys=granges_coding$GENEID, keytype="ENTREZID", columns=c("SYMBOL", "GENENAME","ENSEMBL")) cbind(elementMetadata(granges_coding), annots) ## -------------------------------------------------------------------------- sessionInfo()