get_started: Initiate a DESdemonA project
In FrancisCrickInstitute/DESdemonA: DESeq2 Wrapper For Pre-Specified Analyses

get_started

R Documentation

Initiate a DESdemonA project

Description

Populate a folder with DESdemonA starter scripts

Usage

get_started(
  files = dir(system.file("templates", package = "DESdemonA")),
  path = ".",
  yml = "",
  overwrite = FALSE,
  file_col = "filename",
  name_col = "name",
  ...
)

Arguments

`files`	Which files to retreive from the DESdemonA project
`path`	Where to copy the files to

Details

To start a DESdemonA-based project, we provide a sample set of scripts to point you in the right direction. Firstly there is an '00_init.r' file that will create a universal DESeqDataSet object from your quantified counts file. You may need to edit this to link it to where your quantification pipeline stores its results, and to ensure that the full set of metadata is inserted into the colData.

There is an example '.spec' file - rename and use this as a basis for your statistical analysis plan, or if you have an existing one, delete the example one and copy the existing one into the folder instead.

The main analysis is run via "01_analyse.r" - you should render this via rmarkdown. It will look for every '.spec' file in the current directory.

There will also be a "02_further_steps.r" script at some point. This will give concrete examples of how you might want to extract results for further programmatic use, to build upon the html report that rendering the "01_analyse.r" will provide.

There's also a DESCRIPTION file, so that it is easy to turn your analysis into a re-distributable R package.

The recommended usage is, at the start of project development, to simply call 'DESdemonA::get_started()' in the relevant directory, as the defaults path and files are sufficient - it will refuse to overwrite existing files, so is safe in that sense.