organismData: Organism data

In jasenfinch/riches: Strucutral and Functional Enrichment Analyses

Organism data

Description

Load or build the organism specific KEGG datafor enrichment analysis. This provides a convenience wrapper around FELLA::loadKEGGdata, FELLA::buildGraphFromKEGGREST and FELLA::buildDataFromGraph. See the documentation of these functions for further information.

Usage

organismData(
  organism,
  methods = availableMethods(),
  filter_path = NULL,
  database_directory = organism,
  internal_directory = TRUE,
  damping_factor = 0.85,
  niter = 100
)

Arguments

organism	the KEGG code for the organism of interest
methods	the enrichment techniques to build. Any returned by availableMethods.
filter_path	argument to pass to argument filter.path of FELLA::buildGraphFromKEGGREST. A vector of regular expressions to match pathways to exclude.
database_directory	argument to pass to argument databaseDir of FELLA::buildDataFromGraph and FELLA::loadKEGGdata. The directory name/path in which to save the KEGG data.
internal_directory	logical. Argument to pass to argument internalDir of FELLA::buildDataFromGraph and FELLA::loadKEGGdata. Should the save directory be internal to the FELLA package directory?
damping_factor	argument to pass to argument dampingFactor of FELLA::buildDataFromGraph. A value between 0 and 1 for the PageRank damping factor.
niter	argument to pass to argument niter of FELLA::buildDataFromGraph. A value between 10 and 1000. The number of iterations to estimate the values for CC size.

Value

An object of S4 class FELLA.DATA containing the KEGG data for the specified organism.

Examples

## Load the example organism data available from within the package
organismData(
  'bdi',
  database_directory = system.file(
    'bdi',
    package = 'riches'),
  internal_directory = FALSE
)

jasenfinch/riches documentation built on April 24, 2023, 9:45 a.m.