## ----设置，回声=假-------------------------------------------- knitr :: opts_chunk $ set（cache = true）## ---- Phix ----------------------------------------------------------------------------------------------------------------phix174phage）## ----共识----------------------------------------------- M < - Cancsensusmatrix（phix174phage）[1：4，]多态性< - 哪个（COLSUMS（M！= 0）> 1）Mapply（Substr，多态，多晶型，Moreargs =列表（x = phix174phage））## ----范围，消息= false ------------------------------------------------- - 需要（基因组）GR < - GRANGES（“A”，讽刺（C（10,20,22），宽度= 5），“+”）偏移（GR，1）＃1的坐标！范围（gr）＃内部范围减少（gr）＃范围内覆盖（gr）setdiff（范围（gr），gr）＃'内含子'## ---- bsgenome - request，message = false ---------------------------------（bsgenome.hsapiens.ucsc.hg19）chr14_range = granges（“chr14”，讽刺（1，SEQLENGTHS（HSAPIENS）[“CHR14”]））CHR14_DNA < - GETSEQ（HSAPIENS，CHR14_RANGE）LEDITYREQUCEY（CHR14_DNA，“GC”，AS.PROB = TRUE）## ---- BAM - 要求 ----------------------------------------------------------------------需要（基因组）要求（基因组）要求（RSAMTOOLS）##我们的利益地区的ROI < - GRANGES（“CHR14”，讽刺（19653773，宽度= 1））##样本数据要求（'rnaseqdata.hnrnpc.bam.chr14'）bf < - bamfile（rnaseqdata.hnrnpc.bam.chr14_bamfiles [[1]]，asmates = true）##对齐，结，重叠我们的ROI Paln < - ReadGalignmentsList（BF）J < -汇总junctions（paln，with.revmap = true）j_overlap < - j [j％over％roi] ##支持读Paln [J_Overlap $ RevMap [[1]] ## ---- VCF，消息=假---------------------------------------------- ## 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(rowData(vcf), TxDb.Hsapiens.UCSC.hg19.knownGene, CodingVariants()) head(coding) ## ----summarizeOverlaps-roi, message=FALSE-------------------------------- require(TxDb.Hsapiens.UCSC.hg19.knownGene) exByGn <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, "gene") ## only chromosome 14 seqlevels(exByGn, force=TRUE) = "chr14" ## ----summarizeOverlaps-bam, message=FALSE-------------------------------- require(RNAseqData.HNRNPC.bam.chr14) length(RNAseqData.HNRNPC.bam.chr14_BAMFILES) ## ----summarizeOverlaps--------------------------------------------------- ## next 2 lines optional; non-Windows library(BiocParallel) register(MulticoreParam(workers=detectCores())) olaps <- summarizeOverlaps(exByGn, RNAseqData.HNRNPC.bam.chr14_BAMFILES) ## ----summarizeOverlaps-explore------------------------------------------- olaps head(assay(olaps)) colSums(assay(olaps)) # library sizes plot(sum(width(olaps)), rowMeans(assay(olaps)), log="xy") ## ----summarizeOverlaps-gc------------------------------------------------ require(BSgenome.Hsapiens.UCSC.hg19) sequences <- getSeq(BSgenome.Hsapiens.UCSC.hg19, rowData(olaps)) gcPerExon <- letterFrequency(unlist(sequences), "GC") gc <- relist(as.vector(gcPerExon), sequences) gc_percent <- sum(gc) / sum(width(olaps)) plot(gc_percent, rowMeans(assay(olaps)), log="y")