## ----style, echo = FALSE, results = 'asis'------------------------------- BiocStyle::markdown() ## ---- echo=FALSE, results="hide"----------------------------------------- # Ensure that any errors cause the Vignette build to fail. library(knitr) opts_chunk$set(error=FALSE) ## ---- echo = FALSE------------------------------------------------------- apiKey <- Sys.getenv("GOOGLE_API_KEY") if (nchar(apiKey) == 0) { warning(paste("To build this vignette, please setup the environment variable", "GOOGLE_API_KEY with the public API key from your Google", "Developer Console before loading the GoogleGenomics package,", "or run GoogleGenomics::authenticate.")) knitr::knit_exit() } ## ----message=FALSE------------------------------------------------------- library(GoogleGenomics) # This vignette is authenticated on package load from the env variable GOOGLE_API_KEY. # When running interactively, call the authenticate method. # ?authenticate ## ------------------------------------------------------------------------ reads <- getReads() length(reads) ## ------------------------------------------------------------------------ class(reads) mode(reads) ## ------------------------------------------------------------------------ names(reads[[1]]) ## ------------------------------------------------------------------------ reads[[1]]$alignedSequence reads[[1]]$alignment$position$referenceName reads[[1]]$alignment$position$position ## ------------------------------------------------------------------------ readsToGAlignments(reads) ## ------------------------------------------------------------------------ # Change the values of 'chromosome', 'start', or 'end' here if you wish to plot # alignments from a different portion of the genome. alignments <- getReads(readGroupSetId="CMvnhpKTFhDyy__v0qfPpkw", chromosome="chr13", start=33628130, end=33628145, converter=readsToGAlignments) alignments ## ----message=FALSE------------------------------------------------------- library(ggbio) ## ----coverage------------------------------------------------------------ alignmentPlot <- autoplot(alignments, aes(color=strand, fill=strand)) coveragePlot <- ggplot(as(alignments, "GRanges")) + stat_coverage(color="gray40", fill="skyblue") tracks(alignmentPlot, coveragePlot, xlab="Reads overlapping rs9536314 for NA12893") ## ----ideogram------------------------------------------------------------ ideogramPlot <- plotIdeogram(genome="hg19", subchr="chr13") ideogramPlot + xlim(as(alignments, "GRanges")) ## ------------------------------------------------------------------------ sessionInfo()