## ----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"，警告= FALSE --------------------------------------------------- suppressPackageStartupMessages({库(GenomicRanges)图书馆(GenomicAlignments)图书馆(Biostrings)图书馆(Rsamtools)图书馆(ShortRead)图书馆(BiocParallel)图书馆(rtracklayer)图书馆(VariantAnnotation)图书馆(AnnotationHub)图书馆(BSgenome.Hsapiens.UCSC.hg19)图书馆(RNAseqData.HNRNPC.bam.chr14)})啊= AnnotationHub () ## ---- eval = FALSE ----------------------------------------------------------------------------------- #帮助(包=“GenomicRanges”)(包= " GenomicRanges #一幕 ") ## ---- 消息= FALSE -------------------------------------------------------------------------------- 库(Biostrings) d < - DNAString (TTGAAAA-CTC-N)长度(d) #没有字母DNAString # # - eval = FALSE ----------------------------------------------------------------------------------- # 库(AnnotationHub) #啊< - AnnotationHub () # #------------------------------------------------------------------------------------------------- ah2 < -查询(啊,c(“fasta”、“智人”、“运用”、“互补”))dna < - ah2[[“AH68262”]]dna ## ------------------------------------------------------------------------------------------------- getSeq (dna ) ## ------------------------------------------------------------------------------------------------- 库(BSgenome.Hsapiens.UCSC.hg19) chr14_range =农庄(“chr14 IRanges (1,seqlengths (Hsapiens) [" chr14 "])) chr14_dna < - getSeq (Hsapiens chr14_range) letterFrequency (chr14_dna, GC, as.prob = TRUE) # # - eval = FALSE ----------------------------------------------------------------------------------- # ## 1。附加ShortRead和BiocParallel #库(ShortRead) #库(BiocParallel) ## ## 2。创建一个文件路径的向量# fls <- dir("~/fastq"， pattern="*fastq"， full=TRUE) ## ##收集统计# stats0 <- qa(fls) ## ##生成和浏览报告#如果(互动())# browseURL(报告(stats0 )) ## ------------------------------------------------------------------------------------------------- ## 1。加载软件包库(genome icranges)库(genome icalignments) ## 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()