# #——风格,回声= FALSE,结果= '飞机 '--------------------------------- knitr: opts_chunk设置(eval = as.logical (Sys美元。采用“KNITR_EVAL”,“真正的”)),缓存= as.logical (Sys。采用“KNITR_CACHE”、“真的 "))) ## -------------------------------------------------------------------------- x < - rnorm (50) y < - x + rnorm (50) df < - data.frame(它= x, Dep = y)符合< - lm (Dep ~它,df)总结(健康 ) ## ---- 警告= FALSE -------------------------------------------------------- 图书馆(ggplot2) ggplot (df, aes (x = Dep,它的y =)) + geom_point () + geom_smooth(方法= " lm ") ## -------------------------------------------------------------------------- suppressPackageStartupMessages({库(Biostrings)}) dna < - DNAStringSet (c(“AAACTG”,“CCCAACCA”))dna reverseComplement (dna ) ## -------------------------------------------------------------------------- suppressPackageStartupMessages({库(GenomicRanges)}) gr < -农庄(c(“chr1:10-19”、“chr1:15-24”,gr chr1:30-39)) ## -------------------------------------------------------------------------- 宽度(gr ) ## -------------------------------------------------------------------------- 转变(gr, 1)转变(gr, c(1、2、3所示 )) ## -------------------------------------------------------------------------- 空白(gr)减少(gr)分离(gr)(覆盖(gr),“农庄 ") ## -------------------------------------------------------------------------- snp < -农庄(“chr1 IRanges (c(7、12、17、22),宽度= 1))单核苷酸多态性countOverlaps (gr, snp) subsetByOverlaps (snps, gr ) ## -------------------------------------------------------------------------- gr $ p。值< - runif gr (3) ## -------------------------------------------------------------------------- 基因< - c(“A”、“A”、“B”)grl < - splitAsList grl (gr、基因) ## -------------------------------------------------------------------------- gr1一起< - unlist (grl use.names = FALSE) gr1一起neg.log10美元。pvalue < - log10 (gr1一起p.value美元)重新刊登(grl gr1一起 ) ## -------------------------------------------------------------------------- suppressPackageStartupMessages({库(气管)})数据(气管)气道 ## -------------------------------------------------------------------------- colData(气管)气道,气道$敏捷= = "泰爱泰党 "] ## -------------------------------------------------------------------------- rowRanges构成了rowData(气管)$ p(气管)。值< - runif (nrow(气道 )) ## -------------------------------------------------------------------------- libSize < - colSums(化验(气管))libSize气道libSize < - libSize表(rowSums(化验(气管))! = 0 ) ## -------------------------------------------------------------------------- suppressPackageStartupMessages({库(org.Hs.eg.db)})rowData(气管)$符号< - mapIds (org.Hs.eg.db, rownames(气管),“象征”、“运用” " ) ## ---- 警告= FALSE,消息= FALSE ----------------------------------------- suppressPackageStartupMessages({库(AnnotationHub)库(ExperimentHub)})查询(AnnotationHub (), c(“智人”、“gtf”、“发布- 90”))查询(AnnotationHub (), "EnsDb") query(ExperimentHub(), "curatedMetagenomic")