## ----init, eval=TRUE, results='hide', echo=FALSE, cache=FALSE----------------- knitr::opts_chunk$set(cache=FALSE, echo=FALSE, eval=TRUE) ## ----style-knitr, results="asis"------------------------------------------- BiocStyle::latex() ## ----load-package, echo=TRUE, results='hide'------------------------------- library(rDGIdb) ## ----gene-list, echo=TRUE, results='hide'---------------------------------- genes <- c("TNF", "AP1", "AP2", "XYZA") ## ----query-dgidb-first, echo=TRUE, results='hide'-------------------------- result <- queryDGIdb(genes) ## ----access-result-details, echo=TRUE, results='hide'---------------------- ## Result summary resultSummary(result) ## Detailed results detailedResults(result) ## By gene byGene(result) ## Search term summary searchTermSummary(result) ## ----query-dgidb-stab, echo=TRUE, results='hide'--------------------------- queryDGIdb(genes = genes, sourceDatabases = NULL, geneCategories = NULL, interactionTypes = NULL) ## ----argument-options, echo=TRUE, results='markup'------------------------- ## Available source databases sourceDatabases() ## Available gene categories geneCategories() ## Available interaction types interactionTypes() ## ----query-dgidb-optional, echo=TRUE, results='hide'----------------------- resultFilter <- queryDGIdb(genes, sourceDatabases = c("DrugBank","MyCancerGenome"), geneCategories = "CLINICALLY ACTIONABLE", interactionTypes = c("suppressor","activator","blocker")) ## ----bp-figure-setup, echo=FALSE, results='hide'--------------------------- h <- '0.5\\linewidth' w <- '0.7\\linewidth' c <- 'center' ## ----bp,echo=TRUE,fig.align=c,fig.height=5,fig.width=7,out.height=h,out.width=w---- plotInteractionsBySource(result, main = "Number of interactions by source") ## ----resource-versions, echo=FALSE, results='hide'------------------------- resourceVersions() ## ----variant-annotation, echo=TRUE, results='hide', eval=FALSE------------- # library("VariantAnnotation") # library("TxDb.Hsapiens.UCSC.hg19.knownGene") # library("org.Hs.eg.db") # vcf <- readVcf("file.vcf.gz", "hg19") # seqlevels(vcf) <- paste("chr", seqlevels(vcf), sep = "") # rd <- rowRanges(vcf) # loc <- locateVariants(rd, TxDb.Hsapiens.UCSC.hg19.knownGene, CodingVariants()) # symbols <- select(x = org.Hs.eg.db, keys = mcols(loc)$GENEID, # columns = "SYMBOL", keytype = "ENTREZID") # genes <- unique(symbols$SYMBOL) ## ----questions, echo=TRUE, results='hide'---------------------------------- ?queryDGIdb ?rDGIdbFilters ?rDGIdbResult ?plotInteractionsBySource ## ----session-info, results="asis"------------------------------------------ toLatex(sessionInfo()) ## ----citation, echo=TRUE, results='hide'----------------------------------- citation('rDGIdb')