# #设置,回声= FALSE,结果=“隐藏 "---------------------------------------- 库(BiocStyle) knitr: opts_chunk设置美元(整洁= FALSE, dev =“png”,消息= FALSE,错误= FALSE,警告= TRUE) # #——加载数据 ---------------------------------------------------------------- 图书馆(DEGreport)数据(humanGender) # #——实验 --------------------------------------------------------------- 库(DESeq2) idx < - c (1:10, 75:85) dds < - DESeqDataSetFromMatrix(化验(humanGender) [[1]] [1:1000 idx],colData (humanGender) [idx、)、设计dds < - = ~集团)DESeq (dds) res < -结果(dds) # #——count-design ------------------------------------------------------------- 计数< -计数(dds,规范化= TRUE)设计< - as.data.frame (colData (dds )) ## ---- check-factor ------------------------------------------------------------- degCheckFactors(计数[1:6 ]) ## ---- 质量控制 ----------------------------------------------------------------------- degQC(数量、设计(“集团”),pvalue pvalue = res[[” "]]) ## ---- 浸 ---------------------------------------------------------------------- resCov < degCovariates (log2(计数(dds) + 0.5), colData (dds )) ## ---- corcov ------------------------------------------------------------------- 和< degCorCov (colData (dds))的名字(软木)# #——报告,eval = FALSE ------------------------------------------------------- # createReport (colData (dds)[[“集团”]],计数(dds,规范化= TRUE), # row.names (res) [1:20], res[[“pvalue”]],路径= " ~ /下载 ") ## ---- degComps ----------------------------------------------------------------- 度< - degComps (dds,梳子=“集团”,对比=列表(“group_Male_vs_Female”,c(“集团”,“女性”,“男性”)))名称(度)# #——度 ---------------------------------------------------------------------- 度(度[[1 ]]) ## ---- 生 ---------------------------------------------------------------------- 度(度[[1]],“生”,“宠物猫 ") ## ---- 意义 ------------------------------------------------------------- 意义(度[[1]],fc = 0,罗斯福= 0.05)# #——significants-list -------------------------------------------------------- 意义(度,fc = 0,罗斯福= 0.05)# #——significants-list-full --------------------------------------------------- 意义(fc = 0度,罗斯福= 0.05,= TRUE) # #——plotMA ------------------------------------------------------------------- degMA(度[[1]],diff = 2,限制= 3)# #——plotMA-raw --------------------------------------------------------------- degMA(度[[1]],diff = 2,限制= 3,原始= TRUE) # #——plotMA-cor --------------------------------------------------------------- degMA(度[[1]],限制= 3,相关性= TRUE) # #——deseq2-volcano ----------------------------------------------------------- res [[" id "]] < - row.names (res) < - as.data.frame (res [1:10, c(“log2FoldChange”、“padj”,“id”)])degVolcano (res (c(“log2FoldChange”、“padj”)],plot_text =) # #——deseq2-gene-plots展示 -------------------------------------------------------- degPlot (dds = dds, res = res, n = 6, x = " ") ## ---- deseq2-gene-plot-wide ---------------------------------------------------- degPlotWide (dds rownames (dds)[1:5],组= "组 ") ## ---- 标记 ------------------------------------------------------------------ 数据(geneInfo) degSignature (humanGender geneInfo,组= "组 ") ## ---- deseq2 ------------------------------------------------------------------- resreport < - degResults (dds = dds,名称=“测试”,组织= NULL, do_go = FALSE,组=“集团”,x =“集团”,path_results = NULL) # #,闪亮的eval = FALSE -------------------------------------------------------- # degObj(计算、设计、“degObj.rda”)#库(亮)#亮::runGitHub(“lpantano /亮”,子目录= "表情 ") ## ---- 模式 ------------------------------------------------------------------ 马=测定(rlog (dds)) [row.names (res) [1:10]] res < - degPatterns(马、设计时间= " ") ## ---- 过滤,结果= "飞机 "--------------------------------------------------- 猫(“基因原始数矩阵:1000”)filter_count < - degFilter(计数(dds)、设计、“组”,最小值= 1,minreads = 50)猫(“基因最终计算矩阵”,nrow (filter_count )) ## ---- degColors ---------------------------------------------------------------- 库(ComplexHeatmap) th < - HeatmapAnnotation (df = colData (dds) = degColors上校(colData (dds),真的))的热图(log2(计数(dds) + 0.5) [1:10,], top_annotation = th)图书馆(pheatmap) pheatmap (log2(计数(dds) + 0.5) [1:10,], annotation_col = as.data.frame (colData (dds)) [1:4], annotation_colors = degColors(colData(dds)[1:4], con_values = c("white", "red") ) ) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()