## ----style, echo = FALSE, results = 'asis'------------------------------- knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")) ) options(width = 75) ## ------------------------------------------------------------------------ BiocManager::available("^org\\.") ## ---- message = FALSE---------------------------------------------------- library(AnnotationHub) ## ------------------------------------------------------------------------ query(AnnotationHub(), "^org\\.") ## ---- message = FALSE---------------------------------------------------- library(org.Hs.eg.db) ## ------------------------------------------------------------------------ head(keys(org.Hs.eg.db)) ## ------------------------------------------------------------------------ eid <- sample(keys(org.Hs.eg.db), 10) ## ------------------------------------------------------------------------ mapIds(org.Hs.eg.db, eid, "SYMBOL", "ENTREZID") ## ------------------------------------------------------------------------ map <- select(org.Hs.eg.db, eid, c("SYMBOL", "GO"), "ENTREZID") dim(map) head(map) ## ---- message = FALSE---------------------------------------------------- library(GO.db) ## ---- message=FALSE------------------------------------------------------ library(dplyr) # for `%>%` ## ------------------------------------------------------------------------ BiocManager::available("^TxDb") %>% tibble::enframe(name = NULL) ## ------------------------------------------------------------------------ query(AnnotationHub(), "^TxDb\\.") ## ---- message = FALSE---------------------------------------------------- library(TxDb.Hsapiens.UCSC.hg38.knownGene) ## ------------------------------------------------------------------------ exons(TxDb.Hsapiens.UCSC.hg38.knownGene) ## ------------------------------------------------------------------------ ex <- exons(TxDb.Hsapiens.UCSC.hg38.knownGene, columns = "GENEID") ex ## ------------------------------------------------------------------------ std_ex <- keepStandardChromosomes(ex, pruning.mode="coarse") std_ex ## ------------------------------------------------------------------------ table(seqnames(std_ex)) ## ------------------------------------------------------------------------ std_ex[width(std_ex) > 10000] ## ---- message = FALSE---------------------------------------------------- library(ensembldb) ## ------------------------------------------------------------------------ query(AnnotationHub(), c("^EnsDb\\.", "Ensembl 96")) ## ---- message = FALSE---------------------------------------------------- library(biomaRt) ## ----biomart, eval=FALSE------------------------------------------------- ## library(biomaRt) ## head(listMarts(), 3) ## list marts ## head(listDatasets(useMart("ensembl")), 3) ## mart datasets ## ensembl <- ## fully specified mart ## useMart("ensembl", dataset = "hsapiens_gene_ensembl") ## ## head(listFilters(ensembl), 3) ## filters ## myFilter <- "chromosome_name" ## substr(filterOptions(myFilter, ensembl), 1, 50) ## return values ## myValues <- c("21", "22") ## head(listAttributes(ensembl), 3) ## attributes ## myAttributes <- c("ensembl_gene_id","chromosome_name") ## ## ## assemble and query the mart ## res <- getBM(attributes = myAttributes, filters = myFilter, ## values = myValues, mart = ensembl) ## ---- message = FALSE---------------------------------------------------- library(KEGGREST) ## ---- message = FALSE---------------------------------------------------- library(AnnotationHub) ah <- AnnotationHub() ## ------------------------------------------------------------------------ query(ah, "^org\\.") ## ------------------------------------------------------------------------ ah["AH70563"] ## ------------------------------------------------------------------------ org <- ah[["AH70563"]] org ## ------------------------------------------------------------------------ chooseCentralOrgPkgSymbol(org) columns(org) ## ---- message = FALSE---------------------------------------------------- library(dplyr) # for `%>%` ## ------------------------------------------------------------------------ eid <- head(keys(org)) AnnotationDbi::select(org, eid, "SYMBOL", "ENTREZID") eid %>% mapIds(x = org, "SYMBOL", "ENTREZID") %>% tibble::enframe("ENTREZID", "SYMBOL") ## ---- message = FALSE---------------------------------------------------- library(ExperimentHub) library(curatedTCGAData) ## ------------------------------------------------------------------------ curatedTCGAData() curatedTCGAData("BRCA") curatedTCGAData("BRCA", c("RNASeqGene", "CNVSNP")) ## ---- message = FALSE---------------------------------------------------- mae <- curatedTCGAData("BRCA", c("RNASeqGene", "CNVSNP"), dry.run=FALSE) mae ## ------------------------------------------------------------------------ mae[["BRCA_RNASeqGene-20160128"]] %>% assay() %>% colSums() %>% density() %>% plot(main = "TCGA BRCA RNASeq Library Size") ## ---- message = FALSE---------------------------------------------------- library(VariantAnnotation) ## ---- message = FALSE---------------------------------------------------- library(ensemblVEP) ## ------------------------------------------------------------------------ sessionInfo()