# #设置,回声= FALSE --------------------------------------------------- 库(LearnBioconductor) stopifnot (BiocInstaller:: biocVersion() = = 3.1” ") ## ---- 风格,回声= FALSE,结果= '飞机 '------------------------------- BiocStyle:减价()knitr: opts_chunk设置(整洁= FALSE) # #美元——Biostrings消息= FALSE ------------------------------------------- suppressPackageStartupMessages({库(Biostrings)})数据(phiX174Phage) #样本数据,phiX174Phage m <- consensusMatrix(phiX174Phage)[1:4，] #核。x位置计数多态<——(colSums (m ! = 0) > 1) m(多态)# #——showMethods eval = FALSE --------------------------------------------- # showMethods(类类(phiX174Phage) =, =搜索 ()) ## ---- eg-GRanges ---------------------------------------------------------- ## ' 注释的包;以后……suppressPackageStartupMessages({library(TxDb.Hsapiens.UCSC.hg19.knownGene)}) promoters <- promoters(TxDb.Hsapiens.UCSC.hg19.knownGene) ## 'GRanges' with 2元数据列promoters head(table(seqnames(promoters))) table(strand(promoters)) seqinfo(promoters) ##类载体访问启动子[seqnames(promoters) %in% c("chr1"， "chr2")] ##元数据mcols(promoters) length(unique(promoters$tx_name)) ## ----eg-GRangesList------------------------------------------------------ ## exons，按转录文本exByTx <- exonsBy(TxDb.Hsapiens.UCSC.hg19)分组。knownGene， "tx"， use.names=TRUE) ## list-like subsetting exByTx[1:10] # also logical, character，…uc001aaa exByTx[[”。3"]] #也numeric ##访问器返回type - list，例如，IntegerList width(exByTx) log10(width(exByTx)) ##容易问基本的问题，例如，…hist(unlist(log10(width(exByTx)))) # expons的宽度exByTx[it .max(max(width(exByTx)))] #最大外显子exByTx[it .max(elementlength (exByTx))] #最外显子的transcript ## ----eg-ExpressionSet---------------------------------------------------- suppressPackageStartupMessages({library(ALL)}) data(ALL) ALL ## '表型'(样本)和'特征'数据头(pData(ALL))头(featureNames(ALL)) ##访问pData列; matrix-like subsetting; exprs() ALL[, ALL$sex %in% "M"] range(exprs(ALL)) ## 30% 'most variable' features (c.f., genefilter::varFilter) iqr <- apply(exprs(ALL), 1, IQR) ALL[iqr > quantile(iqr, 0.7), ] ## ----eg-SummarizedExperiment--------------------------------------------- suppressPackageStartupMessages({ library(airway) }) data(airway) airway ## column and row data colData(airway) rowData(airway) ## access colData; matrix-like subsetting; assay() / assays() airway[, airway$dex %in% "trt"] head(assay(airway)) assays(airway) ## library size colSums(assay(airway)) hist(rowMeans(log10(assay(airway)))) ## ----gc-reference-------------------------------------------------------- library(BSgenome.Hsapiens.UCSC.hg19) chr1seq <- BSgenome.Hsapiens.UCSC.hg19[["chr1"]] chr1alf <- alphabetFrequency(chr1seq) chr1gc <- sum(chr1alf[c("G", "C")]) / sum(chr1alf[c("A", "C", "G", "T")]) ## ----gc-exons-1---------------------------------------------------------- library(TxDb.Hsapiens.UCSC.hg19.knownGene) genes <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene) genes1 <- genes[seqnames(genes) %in% "chr1"] seq1 <- getSeq(BSgenome.Hsapiens.UCSC.hg19, genes1) alf1 <- alphabetFrequency(seq1, collapse=TRUE) gc1 <- sum(alf1[c("G", "C")]) / sum(alf1[c("A", "C", "G", "T")]) ## ----gc-exons-2---------------------------------------------------------- alf2 <- alphabetFrequency(seq1, collapse=FALSE) gc2 <- rowSums(alf2[, c("G", "C")]) / rowSums(alf2[,c("A", "C", "G", "T")]) ## ----gc-denisty---------------------------------------------------------- plot(density(gc2)) abline(v=c(chr1gc, gc1), col=c("red", "blue"), lwd=2) ## ----airway-plot--------------------------------------------------------- iqr <- apply(assay(airway), 1, IQR) airway1 <- airway[iqr > quantile(iqr, 0.7),] plot(density(rowMeans(asinh(assay(airway1))))) ## ----airway-rowttest----------------------------------------------------- suppressPackageStartupMessages({ library(genefilter) }) ttest <- rowttests(asinh(assay(airway1)), airway1$dex) ttest$p.adj <- p.adjust(ttest$p.value, method="BH") ttest[head(order(ttest$p.adj)),] split(assay(airway1)[order(ttest$p.adj)[1], ], airway1$dex) ## ----airway-merge-------------------------------------------------------- mcols(rowData(airway1)) <- ttest head(mcols(airway1))