Nothing
## ----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()
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