## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"-------------------- BiocStyle::latex() ## ----setup, include=FALSE, cache=FALSE------------------------------------- library(knitr) opts_chunk$set(out.width="0.7\\maxwidth",fig.align="center") ## ----load_bsgenome, message=FALSE------------------------------------------ library(BSgenome.Hsapiens.UCSC.hg38) g <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 ## ----load_branchpointer, message=FALSE------------------------------------- library(branchpointer) ## ----read_exon_gtf, message=FALSE, eval=FALSE------------------------------ # exons <- gtfToExons("gencode.v26.annotation.gtf") ## ----read_exon_small, message=FALSE---------------------------------------- smallExons <- system.file("extdata","gencode.v26.annotation.small.gtf", package = "branchpointer") exons <- gtfToExons(smallExons) ## ----show_introns, message=FALSE------------------------------------------- queryIntronFile <- system.file("extdata","intron_example.txt", package = "branchpointer") queryIntronTable <- read.delim(queryIntronFile) head(queryIntronTable) ## ----read_introns, message=FALSE------------------------------------------- queryIntron <- readQueryFile(queryIntronFile, queryType = "region", exons = exons) head(queryIntron) ## ----make_intron, message=FALSE-------------------------------------------- queryIntronFromGTF <- makeBranchpointWindowForExons("ENSE00000939171.1", idType = "exon_id", exons = exons) head(queryIntronFromGTF) # for multiple ids: queryIntronFromGTF <- makeBranchpointWindowForExons(c("ENSE00000939171.1", "ENSE00001814242.1"), idType = "exon_id", exons = exons) head(queryIntronFromGTF) ## ----predict_introns, message=FALSE---------------------------------------- branchpointPredictionsIntron <- predictBranchpoints(queryIntron, queryType = "region", BSgenome = g) head(branchpointPredictionsIntron) ## ----brca2-plot------------------------------------------------------------ plotBranchpointWindow(queryIntron$id[2], branchpointPredictionsIntron, probabilityCutoff = 0.52, plotMutated = FALSE, plotStructure = TRUE, exons = exons) ## ----show_snp, message=FALSE----------------------------------------------- querySNPFile <- system.file("extdata","SNP_example.txt", package = "branchpointer") querySNPTable <- read.delim(querySNPFile) head(querySNPTable) ## ----read_snp, message=FALSE----------------------------------------------- querySNP <- readQueryFile(querySNPFile, queryType = "SNP", exons = exons, filter = TRUE) head(querySNP) ## ----read_snp_mart, message=FALSE------------------------------------------ library(biomaRt) mart <- useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp",host="www.ensembl.org") querySNP <- makeBranchpointWindowForSNP(c("rs587776767","rs786205083"), mart.snp = mart, exons = exons, filter = FALSE) head(querySNP) ## ----snp_att_fa, message=FALSE, eval=FALSE--------------------------------- # branchpointPredictionsSNP <- predictBranchpoints(querySNP, # queryType = "SNP", # genome = "GRCh38.primary_assembly.genome.fa", # bedtoolsLocation="/Apps/bedtools2/bin/bedtools") ## ----snp_att_BS, message=FALSE--------------------------------------------- #for query SNPs branchpointPredictionsSNP <- predictBranchpoints(querySNP, queryType = "SNP", BSgenome = g) head(branchpointPredictionsSNP) #to summarise effects: querySNPSummary <- predictionsToSummary(querySNP,branchpointPredictionsSNP) head(querySNPSummary) ## ----rs587776767-plot------------------------------------------------------ plotBranchpointWindow(querySNP$id[2], branchpointPredictionsSNP, probabilityCutoff = 0.52, plotMutated = TRUE, plotStructure = TRUE, exons = exons) ## ----run times, message=FALSE, eval=FALSE---------------------------------- # # # Step times for annotating branchpoints in introns: # gtfToExons() # # user system elapsed # # 41.385 3.848 47.096 # # # Set 1. 294 lincRNA introns on chr22: # makeBranchpointWindowForExons() # # user system elapsed # # 0.196 0.024 0.226 # predictBranchpoints() # # user system elapsed # # 208.934 4.157 225.849 # # # Set 2. 3693 protein coding exons on chr22: # makeBranchpointWindowForExons() # # user system elapsed # # 0.245 0.013 0.261 # predictBranchpoints() # # user system elapsed # # 2332.519 38.266 2482.032 # # # Step times for annotating branchpoints with SNPs: # # 29899 GWAS SNPS # readQueryFile(filter = TRUE) # # user system elapsed # # 5.997 1.608 7.773 # readQueryFile(filter = FALSE) # # user system elapsed # # 1.744 0.427 2.339 # # # 298 filtered SNPS # predictBranchpoints() # # user system elapsed # # 172.495 2.485 181.876 # # predictionsToSummary() # # user system elapsed # # 0.057 0.003 0.061 ## ----sessionInfo, eval=TRUE------------------------------------------------ sessionInfo()