run_CALANGO {CALANGO}R Documentation

Run the CALANGO pipeline

Description

This function runs the complete workflow of CALANGO and generates the HTML5 output pages and export files.

Usage

run_CALANGO(
  defs,
  type = "correlation",
  cores = NULL,
  render.report = TRUE,
  basedir = ""
)

Arguments

defs

either a CALANGO-type list object or a path to a text file containing the required definitions (see Details).

type

type of analysis to perform. Currently only "correlation" is supported.

cores

positive integer, how many CPU cores to use (multicore acceleration does not work in Windows systems). Setting this parameter overrides any 'cores' field from 'defs'. Multicore support is currently implemented using the 'parallel' package, which uses forking (which means that multicore support is not available under Windows)

render.report

logical: should a HTML5 report be generated?

basedir

path to base folder to which all relative paths in 'defs' refer to.

Details

The script expects a 'CALANGO'-type list, passed either as an actual list object or as a file path. In the latter case, notice that the file must be a text file with a 'field = value' format. Blank likes and lines starting with '#' are ignored. The function expects the input list to have the following fields:

Value

Updated 'defs' list, containing:

Results are also saved to files under 'defs$output.dir'.

Examples

## Not run: 

## Install any missing BioConductor packages for report generation 
## (only needs to be done once)
# CALANGO::install_bioc_dependencies()

# Retrieve example files
basedir <- tempdir()
retrieve_data_files(target.dir = paste0(basedir, "/data"))
defs <- paste0(basedir, "/data/parameters/parameters_domain2GO_count_less_phages.txt")

# Run CALANGO
res <- run_CALANGO(defs, cores = 2)

## End(Not run)


[Package CALANGO version 1.0.8 Index]