create_tox_universe: Create toxicogenomic universe

In anschue/toxprofileR: Functions for Retrieving Dynamic Toxicogenomic Fingerprints

Description

This function depends on the package "kohonen" to infer a SOM from toxicogenomic data.

Usage

create_tox_universe(dslist, logFC_frame, dimens = 60,
  dist.fct = "manhattan", alpha = c(0.8, 0.005), includearchive = T,
  seed = 2312, output = T)

Arguments

dslist	A list of ELists with smoothed logFC data to include in the learning procedure.
logFC_frame	data.frame with additional logFC to include for map learning
dimens	The dimension of the SOM (default: 60)
dist.fct	The distance function to be used (default: manhattan)
alpha	learning parameter for SOM (default: 0.8, 0.005)
includearchive	logical, should published toxicogenomic data be included into SOM (default: T)
seed	The seed to be used for the intial map
output	logical, should analytical plots be given

Value

A result list containing the som_model, the final input dataset (dataset.SOM), compiled metadata, and ProbeIDs.

anschue/toxprofileR documentation built on Nov. 2, 2019, 1:55 p.m.