## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = FALSE, comment = "#>", eval=TRUE ) ## ---- eval=FALSE-------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("easyreporting") ## ----------------------------------------------------------------------------- library("easyreporting") ## ----------------------------------------------------------------------------- proj.path <- file.path(tempdir(), "bioinfo_report") bioEr <- easyreporting(filenamePath=proj.path, title="bioinfo_report", author=c("Dario Righelli")) ## ----------------------------------------------------------------------------- mkdTitle(bioEr, title="Loading Counts Data") mkdCodeChunkComplete(object=bioEr, message=paste0("geneCounts <- importData(sy", "stem.file('extdata/GSE134118_Table_S3.xlsx',", "package='easyreporting'))"), sourceFilesList=system.file("script/importFunctions.R", package="easyreporting")) ## ----------------------------------------------------------------------------- mkdTitle(bioEr, title="Plot PCA on count data", level=2) mkdCodeChunkComplete(bioEr, message="EDASeq::plotPCA(as.matrix(geneCounts))") ## ----------------------------------------------------------------------------- mkdTitle(bioEr, "Differential Expression Analysis") mkdCodeChunkCommented(bioEr, codeMsg="degList <- applyEdgeRExample(counts=geneCounts, samples=colnames(geneCounts), contrast='Pleura - Broth')", commentMsg=paste0("As we saw from the PCA, the groups are well separated", ", so we can perform a Differential Expression analysis with edgeR."), sourceFilesList=system.file("script/geneFunctions.R", package="easyreporting")) ## ----------------------------------------------------------------------------- mkdTitle(bioEr, "MD Plot of DEGs", level=2) mkdCodeChunkComplete(bioEr, message="limma::plotMD(degList$test)") ## ----------------------------------------------------------------------------- compile(bioEr) ## ----------------------------------------------------------------------------- sessionInfo()