## ----knitr-settings, echo=FALSE------------------------------------------ library(knitr) opts_chunk$set(tidy=FALSE, cache=TRUE) ## ----select, eval=FALSE-------------------------------------------------- ## library(org.Hs.eg.db) ## keytypes(org.Hs.eg.db) ## columns(org.Hs.eg.db) ## egid <- ## select(org.Hs.eg.db, "BRCA1", "ENTREZID", "SYMBOL") ## ----cdsBy, eval=FALSE--------------------------------------------------- ## library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene ## cdsByTx <- cdsBy(txdb, "tx") ## ----extactTranscriptsFromGenome, eval=FALSE----------------------------- ## library(BSgenome.Hsapiens.UCSC.hg19) ## library(GenomicFeatures) ## dna <- extractTranscriptsFromGenome(Hsapiens, cdsByTx) ## ----biomart, eval=FALSE------------------------------------------------- ## library(biomaRt) ## ensembl <- ## discover & use ## useMart("ensembl", dataset="hsapiens_gene_ensembl") ## head(listFilters(ensembl), 3) ## myFilter <- "chromosome_name" ## myValues <- c("21", "22") ## myAttributes <- c("ensembl_gene_id","chromosome_name") ## res <- ## getBM(attributes=myAttributes, filters=myFilter, ## values=myValues, mart=ensembl) ## ----psicquic, eval=FALSE------------------------------------------------ ## library(PSICQUIC) ## ## Query web service for available providers ## psicquic <- PSICQUIC() ## providers(psicquic) # 25 available providers ## ## interactions between TP53 and MYC ## tbl <- ## interactions(psicquic, c("TP53", "MYC"), "9606") ## nrow(tbl) # 7 interactions ## ----AnnotationHub, eval=FALSE------------------------------------------- ## library(AnnotationHub) ## hub <- AnnotationHub() ## hub ## 10511 resources