## ----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( person(given="Dario", family="Righelli", email="fake_email@gmail.com", comment=c(ORCID="ORCIDNUMBER", url="www.fakepersonalurl.com", affiliation="Institute of Applied Mathematics, CNR, Naples, IT", affiliation_url="www.fakeurl.com")), person(given="Claudia", family="Angelini", comment=c(ORCID="ORCIDNUMBER", url="www.fakepersonalurl.com", affiliation="Institute of Applied Mathematics, CNR, Naples, IT", affiliation_url="www.fakeurl.com")) ) ) ## ----------------------------------------------------------------------------- mkdTitle(bioEr, title="Loading Counts Data") mkdCodeChunkComplete(object=bioEr, code=quote(geneCounts <- importData( system.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, code=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()