# #设置,包括= FALSE --------------------------------------------------- knitr: opts_chunk美元集(崩溃= FALSE,评论= " # > ",eval = TRUE ) ## ---- eval = FALSE -------------------------------------------------------------- # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“easyreporting ") ## ----------------------------------------------------------------------------- 图书馆(“easyreporting ") ## ----------------------------------------------------------------------------- 项目。path <- file.path(tempdir()， "bioinfo_report") bioEr <- easyreporting(filenamePath=proj. path)path, title="bioinfo_report"，作者=c(person(given="Dario"， family="Righelli"， email="fake_email@gmail.com"， comment=c(ORCID="ORCIDNUMBER"， url="www.fakepersonalurl.com"，隶属关系=" CNR，那不勒斯，IT应用数学研究所"，affiliation=" www.fakeurl.com"))， person(given="Claudia"， family="Angelini"， comment=c(ORCID="ORCIDNUMBER"， url="www.fakepersonalurl.com"，隶属关系=" CNR，那不勒斯，IT应用数学研究所"，affiliation_url = " www.fakeurl.com ")) ) ) ## ----------------------------------------------------------------------------- mkdTitle(骏,title =“加载项数据”)mkdCodeChunkComplete(对象=骏,代码=报价(geneCounts <——importData(执行(“extdata / GSE134118_Table_S3.xlsx”、包= " easyreporting "))), sourceFilesList =执行(“脚本/ importFunctions。R”、包= " easyreporting ")) ## ----------------------------------------------------------------------------- mkdTitle(骏,title =“阴谋PCA统计数据”,级别= 2)mkdCodeChunkComplete(骏,代码=报价(EDASeq: plotPCA (as.matrix (geneCounts )))) ## ----------------------------------------------------------------------------- mkdTitle(骏,“微分表达式分析”)mkdCodeChunkCommented(骏,代码= " degList < applyEdgeRExample(数量= geneCounts样品= colnames (geneCounts),contrast='Pleura - Broth')”，comment=paste0("正如我们从PCA中看到的那样，这些组被很好地分开了"，"，所以我们可以用edgeR进行微分表达式分析。")，sourceFilesList=system.file("script/geneFunctions. file ."R”、包= " easyreporting ")) ## ----------------------------------------------------------------------------- mkdTitle(骏“MD块度”,级别= 2)mkdCodeChunkComplete(骏,代码= " limma: plotMD (degList $测试 )") ## ---- eval = FALSE -------------------------------------------------------------- # 编译(骏 ) ## ---- 整洁= TRUE --------------------------------------------------------------- sessionInfo ()