run_report: Run DESdemonA Report on existing counts object

In FrancisCrickInstitute/DESdemonA: DESeq2 Wrapper For Pre-Specified Analyses

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

Author(s)

Gavin Kelly

FrancisCrickInstitute/DESdemonA documentation built on Jan. 2, 2023, 8:08 p.m.