# #——风格,eval = TRUE,呼应= FALSE,结果= '飞机 '-------------------------- BiocStyle:乳胶(bibstyle =“unsrt”)# BiocStyle::乳胶 () ## ---- 包括= FALSE --------------------------------------------------------- 库(knitr) opts_chunk美元设置(和谐= TRUE ) ## ---- 包括= FALSE --------------------------------------------------------- 库(knitr) opts_chunk美元集(和合= TRUE,缓存= TRUE,消息= FALSE, out.width = "。55 \ \ textwidth”,回声= TRUE, fig.width = 6, fig.height = 6, fig.align = "中心",结果=“标记”,持有= TRUE ) ## ---- loadLib --------------------------------------------------------------- # 加载包和基因表达数据图书馆(mogsa)数据(NCI60_4arrays) # #——dataDim --------------------------------------------------------------- 酸式焦磷酸钠(NCI60_4arrays昏暗的)# # #——auxiVar检查维度表达数据 --------------------------------------------------------------- tumorType < -酸式焦磷酸钠(strsplit (colnames (NCI60_4arrays安捷伦美元),分裂 ="\\."), "[", 1) colcode < - as.factor (tumorType)水平(colcode) < - c(“红”、“绿色”、“蓝”、“青色”、“橙”、“gray25”、“棕色”、“gray75”、“粉红色”)colcode <——as.character (colcode) # #——mbpca1 fig.cap = "每个潜变量的方差。颜色区分来自不同数据集的贡献。"---- moa <- mbpca(NCI60_4arrays, ncomp = 10, k = "all"， method = "globalScore"， option = "lambda1"， center=TRUE, scale=FALSE, moa =TRUE, svd. "解算器=“快速”,麦克斯特= 1000)情节(农业部、价值=“eig”类型= 2)# #——引导,fig.cap = "排列测试 "-------------------------------------- r < - bootMbpca(农业部、mc.cores = 1, B = 20,取代= FALSE,重新取样= "样本 ") ## ---- mpbca2 ---------------------------------------------------------------- 恐鸟< - mbpca (NCI60_4arrays ncomp = 3, k = 0.1, =“globalScore”方法,选择=λ₁,中心= TRUE,规模= FALSE,恐鸟= TRUE,圣言。解算器=“快速”,麦克斯特= 1000)# #——scoreCor -------------------------------------------------------------- 可控硅< - moaScore(农业部)< -在所moaScore(恐鸟)诊断接头(软木(可控硅[1:3],在所 )) ## ---- plot1 fig.width = 10, fig.height = 6 ------------------------------------- 布局(矩阵(1:2,1 2)情节([1:2],在所坳= colcode pch = 20)传说(“topright”,传说=独特(tumorType)坳=独特(colcode) pch = 20)情节([2:3],在所坳= colcode pch = 20) # #——差距,fig.cap = "差距统计图 "------------------------------------- 差距< - moGap(恐鸟,K.max = 12,集群=“盐酸”)布局(矩阵(1 1 1)差距nClust # #美元——集群,fig.width = 6, fig.height = 3 ------------------------------------ hcl < - hclust (dist(在所))cls < - cutree (hcl, k = 4) clsColor < - as.factor (cls)水平(clsColor) < - c(“红”“蓝”、“橙色”,“粉红色”)clsColor < - as.character ((clsColor))的热图(t ([hcl秩序,美元])在所ColSideColors = colcode hcl美元订单,Rowv = NA,Colv = NA)的热图(t ([hcl秩序,美元])在所ColSideColors = clsColor hcl美元订单,Rowv = NA, Colv = NA) # #——系数 ------------------------------------------------------------------ 基因< - moaCoef nonZeroCoef agilent.V1美元(恐鸟)基因。neg # #——sessionInfo,结果=‘黑名单’,eval = TRUE,回声= TRUE --------------- toLatex (sessionInfo ())