## ----style, echo=FALSE, message=FALSE, warning=FALSE, results="asis"------------------------------ options(width=100) knitr::opts_chunk$set(message = FALSE, error = FALSE, warning = FALSE, fig.width=6, fig.height=4) BiocStyle::markdown() ## ---- echo=FALSE, results="hide", warning=FALSE--------------------------------------------------- suppressPackageStartupMessages({ library(GenomicRanges) library(GenomicAlignments) library(Biostrings) library(Rsamtools) library(ShortRead) library(BiocParallel) library(rtracklayer) library(VariantAnnotation) library(AnnotationHub) library(BSgenome.Hsapiens.UCSC.hg19) library(RNAseqData.HNRNPC.bam.chr14) }) ah = AnnotationHub() ## ----eval=FALSE----------------------------------------------------------------------------------- # help(package="GenomicRanges") # vignette(package="GenomicRanges") ## ----message=FALSE-------------------------------------------------------------------------------- library(Biostrings) d <- DNAString("TTGAAAA-CTC-N") length(d) #no of letters in the DNAString ## ----eval=FALSE----------------------------------------------------------------------------------- # library(AnnotationHub) # ah <- AnnotationHub() ## ------------------------------------------------------------------------------------------------- ah2 <- query(ah, c("fasta", "homo sapiens", "Ensembl", "cdna")) dna <- ah2[["AH68262"]] dna ## ------------------------------------------------------------------------------------------------- getSeq(dna) ## ------------------------------------------------------------------------------------------------- library(BSgenome.Hsapiens.UCSC.hg19) chr14_range = GRanges("chr14", IRanges(1, seqlengths(Hsapiens)["chr14"])) chr14_dna <- getSeq(Hsapiens, chr14_range) letterFrequency(chr14_dna, "GC", as.prob=TRUE) ## ----eval=FALSE----------------------------------------------------------------------------------- # ## 1. attach ShortRead and BiocParallel # library(ShortRead) # library(BiocParallel) # # ## 2. create a vector of file paths # fls <- dir("~/fastq", pattern="*fastq", full=TRUE) # # ## 3. collect statistics # stats0 <- qa(fls) # # ## 4. generate and browse the report # if (interactive()) # browseURL(report(stats0)) ## ------------------------------------------------------------------------------------------------- ## 1. load software packages library(GenomicRanges) library(GenomicAlignments) ## 2. load sample data library('RNAseqData.HNRNPC.bam.chr14') bf <- BamFile(RNAseqData.HNRNPC.bam.chr14_BAMFILES[[1]], asMates=TRUE) ## 3. define our 'region of interest' roi <- GRanges("chr14", IRanges(19653773, width=1)) ## 4. alignments, junctions, overlapping our roi paln <- readGAlignmentsList(bf) j <- summarizeJunctions(paln, with.revmap=TRUE) j_overlap <- j[j %over% roi] ## 5. supporting reads paln[j_overlap$revmap[[1]]] ## ------------------------------------------------------------------------------------------------- library(VariantAnnotation) fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation") vcf <- readVcf(fl, "hg19") ## ------------------------------------------------------------------------------------------------- library(rtracklayer) test_path <- system.file("tests", package = "rtracklayer") test_bed <- file.path(test_path, "test.bed") test <- import(test_bed, format = "bed") test ## ------------------------------------------------------------------------------------------------- sessionInfo()