## ----设置，包括= false ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::opts_chunk$set( collapse = FALSE, comment = "#>", eval=TRUE ) ## ---- eval=FALSE------------------------------------------------------------------------------------------------＃if（！sireseenamespace（“ biocmanager”，悄悄= true））＃install.packages（“ biocmanager”）＃biocmanager :: install（“ easyreporting”）## ------------------------------------------------------------------------------------------------------------------------------------------库（“ Easy Reporting”）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- proj.path <-fie.path（tempdir（），“ bioinfo_report”）bioer <- easyreporting（filenamepath = proj.path，title =“ bioinfo_report”=“ righelli”，email =“ face_email@gmail.com”，comment = c（orcid =“ orcidnumber”，url =“ www.fakepersonalurl.com”，分支机构=“应用数学学院affiliation_url =“ www.fakeurl.com”），person（给定=“ claudia”，family =“ angelini”，comment = c（orcid =“ orcidnumber”，url =“ www.fa”kepersonalurl.com”，隶属关系=“应用数学研究所，CNR，Naples，it”，affiliation_url =“ www.fakeurl.com”）））））## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- mkdtitle（bioer，title =“加载计数数据”）mkdcodechunkcomplete（object = bioer，code，code = quote（geneCounts <-importdata（system.file）（system.file（“ extdata/gse134118_table_s.s.s.s.s.s3.xlsx”），package =“ easyreporting”））），sourcefileslist = system.file（“ script/importfunctions.r”，package =“ easyreporting”））## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- mkdtitle（bioer，title =“ count data in count data”，level = 2）mkdcodechunkcomplete（bioer，code，code = quote = quote（edaseq :: plotpca（as.matrix（genecounts）））））））））））））））））） ## ----------------------------------------------------------------------------- mkdTitle(bioEr, "Differential Expression Analysis") mkdCodeChunkCommented(bioEr, code="degList <- applyEdgeRExample(counts=geneCounts, samples=colnames(geneCounts), contrast='Pleura - Broth')", comment=paste0("As we saw from the PCA, the groups are well separated", ", so we can perform a Differential Expression analysis with edgeR."), sourceFilesList=system.file("script/geneFunctions.R", package="easyreporting")) ## ----------------------------------------------------------------------------- mkdTitle(bioEr, "MD Plot of DEGs", level=2) mkdCodeChunkComplete(bioEr, code="limma::plotMD(degList$test)") ## ---- eval=FALSE-------------------------------------------------------------- # compile(bioEr) ## ---- tidy=TRUE--------------------------------------------------------------- sessionInfo()