## ----风格，回声= FALSE，结果='ASIS'---------------------------生物 - 生物 - 生物 - 生物 - 生物 - Biocstyle：：markdown（）选项（width = 100，max.print = 1000）knitr :: opts_chunk $ set（eval = as.logical（sys.getenv（“knitr_eval”，“true”）），缓存= as.logical（sys.getenv（“knitr_cache”，“true”）））## ----包，eval = true，echo = false，警告= false，message = false ------- suppresspackageStartUpMessages（{库（BiCeMbo2015）图书馆（摘要化）图书馆（Airway）}）## ----------------------------------------------------------------- x < - rnorm（1000）＃原子向量y < - x + rnorm（1000，sd = .5）df < - data.frame（x = x，y = y）＃类'data.frame'plot（y〜x，df）＃泛型图，方法plot.formula fit <- lm（y x，df）#close'lm'方法的对象（class = class（fit））＃内部内部## ----生物探测器，消息= false -------------------------------------- - 需要（生物探测器）＃生物序列数据（phix174phage）＃样本数据，查看？phix174phage phix174phagem < - consensusmatrix（phix174phage）[1：4，]＃Nucl。x位置计数多态< - 哪个（COLSUMS（M！= 0）> 1）M [，多晶型]方法（类=类（PHIX174phage））选择方法（Reversecompumplement，Class（Phix174phage））## ----需要 --------------------------------------------------------------------------图书馆（基因组）## ----帮助，eval = False -------------------------------------------------------------------------------- ## help(package="GenomicRanges") ## vignette(package="GenomicRanges") ## vignette(package="GenomicRanges", "GenomicRangesHOWTOs") ## ?GRanges ## ----BSgenome-require, message=FALSE------------------------------------- require(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) ## ----ranges, message=FALSE----------------------------------------------- require(GenomicRanges) gr <- GRanges("A", IRanges(c(10, 20, 22), width=5), "+") shift(gr, 1) # 1-based coordinates! range(gr) # intra-range reduce(gr) # inter-range coverage(gr) setdiff(range(gr), gr) # 'introns' ## ----bam-require--------------------------------------------------------- require(GenomicRanges) require(GenomicAlignments) require(Rsamtools) ## our 'region of interest' roi <- GRanges("chr14", IRanges(19653773, width=1)) ## sample data require('RNAseqData.HNRNPC.bam.chr14') bf <- BamFile(RNAseqData.HNRNPC.bam.chr14_BAMFILES[[1]], asMates=TRUE) ## alignments, junctions, overlapping our roi paln <- readGAlignmentsList(bf) j <- summarizeJunctions(paln, with.revmap=TRUE) j_overlap <- j[j %over% roi] ## supporting reads paln[j_overlap$revmap[[1]]] ## ----vcf, message=FALSE-------------------------------------------------- ## input variants require(VariantAnnotation) fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation") vcf <- readVcf(fl, "hg19") seqlevels(vcf) <- "chr22" ## known gene model require(TxDb.Hsapiens.UCSC.hg19.knownGene) coding <- locateVariants(rowRanges(vcf), TxDb.Hsapiens.UCSC.hg19.knownGene, CodingVariants()) head(coding) ## ----SummarizedExperiment------------------------------------------------ library(SummarizedExperiment) library(airway) data(airway) airway colData(airway) airway[, airway$dex %in% "trt"]