# # - eval = FALSE --------------------------------------------------------------- # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“fCI ") ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- suppressPackageStartupMessages(库(fCI))库(fCI) ) ## ----------------------------------------------------------------------------- fci.data = data.frame(矩阵(样本(1043 * 6,3:100取代= TRUE),1043年,6))fci.data = total.library.size.normalization (fci.data ) ## ----------------------------------------------------------------------------- fci.data = data.frame(矩阵(样本(1043 * 6,3:100取代= TRUE), 1043年,6))fci.data = trim.size.normalization (fci.data ) ## ----------------------------------------------------------------------------- pkg.path = path.package (fCI)文件名=粘贴(包裹。path， "/extdata/Supp_Dataset_part_2.txt"， sep="" ") if(file.exists(filename)){fci=new("NPCI") fci=find.fci. txt")目标(fci, c(1、2、3),c(4、5、6),文件名 ) } ## ----------------------------------------------------------------------------- (Diff.Expr.Genes Diff.Expr.Genes = show.targets (fci)头 ) ## ----------------------------------------------------------------------------- 人物(fci ) ## ----------------------------------------------------------------------------- fci = find.fci。目标(fci, c(1、2),5、文件名 ) ## ----------------------------------------------------------------------------- 如果(file.exists(文件名)){Diff.Expr.Genes = fCI.call.by.index (c(1、2、3),c(4、5、6),文件名)头(Diff.Expr.Genes ) } ## ---- 结果= ' asis '---------------------------------------------------------- fci.data = data.frame(矩阵(样本(1043 * 6,3:100取代= TRUE), 1043年,6 )) ## ---- 警告= FALSE,消息= FALSE ---------------------------------------- 图书馆(fCI) fCI = = find.fci新(“NPCI”)目标。目标(fci, c(1、2、3),c(4、5、6),fci.data) Diff.Expr.Genes = show.targets(目标)头(Diff.Expr.Genes)数据(目标 ) ## ----------------------------------------------------------------------------- fci = new(“NPCI”)filename2 =粘贴(包裹。path， "/extdata/proteoGenomics.txt"， sep="") if(file.exists(filename2)){targets=find.fci. txt"目标(fci,(1:2,七8)列表,列表(5:6,十一12),filename2) Diff.Expr.Genes = show.targets(目标)头(Diff.Expr.Genes ) } ## ----------------------------------------------------------------------------- proteogenomic.data = read.csv (filename2, 9 = \ t)头(proteogenomic.data ) ## ----------------------------------------------------------------------------- fci = new(“NPCI”)fci = setfCI (fci,七8,十一12,seq (= 1.1, = 3 = 0.1),真正的 ) ## ----------------------------------------------------------------------------- 如果(file.exists (filename2)) {fci = find.fci。目标(fci, 7:8, 11:12, filename2)头(show.targets(fci))}数字(fci)