run_report: Run DESdemonA Report on existing counts object

View source: R/admin.R

run_reportR 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

Author(s)

Gavin Kelly


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