params <- list(isSlides = "no") ## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) AsSlides <- TRUE ## ----results='asis',include=TRUE,echo=FALSE----------------------------------- if(params$isSlides == "yes"){ cat(" class: inverse, center, middle # Genomic Features

--- " ) }else{ cat(" ## Genomic Features --- " ) } ## ----setssssup, eval=FALSE,echo=FALSE----------------------------------------- ## library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## export.gff(TxDb.Hsapiens.UCSC.hg19.knownGene,con = "data/test.gff") ## ----setssssuxxp, eval=FALSE-------------------------------------------------- ## if (!requireNamespace("BiocManager", quietly = TRUE)) ## install.packages("BiocManager") ## ## BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene") ## ----sedfs,eval=TRUE,echo=FALSE----------------------------------------------- suppressPackageStartupMessages(library(TxDb.Hsapiens.UCSC.hg19.knownGene)) ## ----ssaa,eval=FALSE---------------------------------------------------------- ## library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## ----sss,eval=TRUE------------------------------------------------------------ class(TxDb.Hsapiens.UCSC.hg19.knownGene) ## ----sssk,eval=TRUE----------------------------------------------------------- TxDb.Hsapiens.UCSC.hg19.knownGene ## ----ssslkk,eval=TRUE--------------------------------------------------------- myGenes <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene) myGenes ## ----ssslkzassk1,eval=TRUE---------------------------------------------------- myExons <- exons(TxDb.Hsapiens.UCSC.hg19.knownGene) myExons ## ----ssslkzaak1,eval=TRUE----------------------------------------------------- myTranscripts <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene) myTranscripts ## ----ssslkzak1z,eval=TRUE----------------------------------------------------- myCDS <- cds(TxDb.Hsapiens.UCSC.hg19.knownGene) myCDS ## ----ssslkzzk,eval=TRUE------------------------------------------------------- myTranscripts <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene, columns=c("gene_id","tx_id")) myTranscripts[1:2] ## ----ssslfdkzzkjj,eval=TRUE--------------------------------------------------- myPromoters <- promoters(TxDb.Hsapiens.UCSC.hg19.knownGene, upstream=2000,downstream=50) myPromoters[1:2] ## ----ssslkzzzjzkjj,eval=TRUE-------------------------------------------------- transcriptByGenes <- transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by="gene") transcriptByGenes[1:2] ## ----ssslkzzszzkjj,eval=TRUE-------------------------------------------------- # transcriptByGenes$1 or transcriptByGenes[[1]] ## ----ssslkzzzzfkjj,eval=TRUE-------------------------------------------------- exonsByTranscript <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by="tx") exonsByTranscript[1:2] ## ----ssslkzzzzfkkjkjj,eval=TRUE----------------------------------------------- myCustomTxDb <- makeTxDbFromGFF("data/Xkr4.gtf") class(myCustomTxDb) ## ----ssslkzzzzfkaakjkjaj,eval=TRUE-------------------------------------------- myCustomTxDb ## ----sssleekzzzzfkjj,eval=TRUE------------------------------------------------ genes(myCustomTxDb) ## ----ssaaslkzzzzfkjj,eval=TRUE------------------------------------------------ exonsBy(myCustomTxDb,by="gene") ## ----skuysslkzzzzfkjj,eval=TRUE----------------------------------------------- library(rtracklayer) availableGenomes <- ucscGenomes() availableGenomes[1:4,] ## ----ssslkzzzzfkssjj,eval=F,cache=FALSE,message=FALSE------------------------- ## hg18TxDb <- makeTxDbFromUCSC(genome="hg18") ## hg18TxDb ## ----ssslkzzzzfkssjj2, eval=TRUE, echo=F-------------------------------------- #saveDb(hg18TxDb, file="data/hg18txdb.sqlite") hg18TxDb <- loadDb("data/hg18txdb.sqlite") #load(file="data/hg18txdb.RData") hg18TxDb ## ----ssslkzzzzddfkjj,eval=TRUE,cache=TRUE,message=FALSE,warning=FALSE--------- hg18Promoters <- promoters(hg18TxDb,2000,50) ## ----ssslkzzzzdddsdsfkjj,eval=TRUE,cache=TRUE,message=FALSE,warning=FALSE----- export.gff(myCustomTxDb,con="customTxDbb.gff",format="gff") export.gff(myCustomTxDb,con="customTxDbb.gtf",format="gtf") ## ----ssslkzzzzsdsddfkjj,eval=TRUE,cache=TRUE,message=FALSE,warning=FALSE------ transcriptByGenes <- exonsBy(hg18TxDb,by="gene") length(transcriptByGenes) ## ----ssslkzzzzddcccfkjj,eval=TRUE,cache=TRUE,message=FALSE,warning=FALSE------ transcriptNumberPerGene <- lengths(transcriptByGenes) transcriptNumberPerGene[1:5] ## ----ssslkzzxxzssszddfkjj,eval=TRUE,cache=TRUE,message=FALSE,warning=FALSE---- transcript_Lens <- transcriptLengths(hg18TxDb) transcript_Lens[1:5,] ## ----ssslkzzzzddsddfkjj,eval=TRUE,cache=TRUE,message=FALSE,warning=FALSE------ library(BSgenome.Hsapiens.UCSC.hg19) hg19TransSeq <- extractTranscriptSeqs(BSgenome.Hsapiens.UCSC.hg19, transcripts=TxDb.Hsapiens.UCSC.hg19.knownGene) hg19TransSeq ## ----ssslkdszzzzddfkjj,eval=TRUE,cache=TRUE,message=FALSE,warning=FALSE------- writeXStringSet(hg19TransSeq,"myTranscriptSequences.fa") ## ----------------------------------------------------------------------------- library(GenomeInfoDb) ## ----------------------------------------------------------------------------- allMappings <- genomeStyles() names(allMappings) ## ----------------------------------------------------------------------------- #allMappings$Homo_sapiens or allMappings[["Homo_sapiens"]] ## ----------------------------------------------------------------------------- myGenes <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene) seqlevelsStyle(myGenes) myGenes[1:2,] ## ----------------------------------------------------------------------------- seqlevelsStyle(myGenes) <- "Ensembl" myGenes[1:2,] ## ----ssslkdszzzdsdzddfkjjsds,eval=FALSE,echo=TRUE,cache=TRUE,message=FALSE,warning=FALSE---- ## BiocManager::install("org.Hs.eg.db") ## library(org.Hs.eg.db) ## class(org.Hs.eg.db) ## ----ssslkdszzsdzzddfkjjsds,eval=TRUE,echo=FALSE,cache=FALSE,message=FALSE,warning=FALSE---- suppressPackageStartupMessages(library(org.Hs.eg.db)) class(org.Hs.eg.db) ## ---- echo=TRUE, eval=TRUE---------------------------------------------------- columns(org.Hs.eg.db) ## ---- echo=TRUE, eval=TRUE---------------------------------------------------- help(GENENAME) ## ---- echo=TRUE, eval=TRUE---------------------------------------------------- keytypes(org.Hs.eg.db) ## ---- echo=TRUE, eval=TRUE---------------------------------------------------- keys(org.Hs.eg.db, keytype="SYMBOL")[1:10] ## ---- echo=TRUE, eval=TRUE,message=FALSE,warning=FALSE------------------------ select(org.Hs.eg.db, keys = "A1BG", keytype = "SYMBOL", columns = c("SYMBOL", "GENENAME", "CHR") ) ## ----sqsq, echo=TRUE, eval=TRUE, dependson="ssslkzzzzfkssjj"------------------ geneLocations <- genes(hg18TxDb) geneLocations ## ----sqsaq, echo=TRUE, eval=TRUE, dependson="ssslkzzzzfkssjj",message=FALSE,warning=FALSE---- IDs <- geneLocations$gene_id myTable <- select(org.Hs.eg.db, keys = IDs, keytype = "ENTREZID", columns = c("SYMBOL", "GENENAME", "ENTREZID") ) myTable[1:2,]