run_report: Run DESdemonA Report on existing counts object
In crickbabs/RNASeq-DESeq: DESeq2 Wrapper For Pre-Specified Analyses

run_report

R Documentation

Run DESdemonA Report on existing counts object

Description

This will generate a standard report on the DESeq2 data object you provide it. It will store data objects in the data directory, so that will need to be created, as will the results folder.

Usage

run_report(
  dds,
  spec_file,
  results = "results",
  output_file = "analyse.html",
  title = "RNASeq Analysis",
  author = Sys.info["user"]
)

Arguments

`dds`	The DESeqDataSet object that you want to run the report on. It needs the basic set of `colData` columns that are used in the analysis plan. `colnames(dds)` will be used as labels in plot, etc. In addition, if its `mcols` has columns of the that are set to `entrez` and/or `symbol`, these will get added to the report. `metadata(dds)$org <- "org.Mm.eg.db"` will ensure that the correct annotation libraries are used, but this is only strictly necessary for functional annotation (which also requires those additional columns in the `mcols` property.
`spec_file`	The Analaysis Plan
`results`	Directory in which to store excel results
`output_file`	The name of the html report.
`title`	HTML Title of the document
`autor`	The name of the author to appear on the report