create_gen3DNet: Create a general 3D network.

In MollahLab/gen3DNet: An R Package for Generating 3D Network Models

Create a general 3D network.

Description

This function performs calculations to generate a 3D network. It is not meant to be called directly. You should use the gen3DNet function, which sanitizes arguments and reads in data from file paths. See help(gen3DNet) for further documentation.

Usage

create_gen3DNet(
  left,
  right,
  nmf_nrun = 10,
  k = c(),
  k_picker = max_ward_kl,
  seed = 123456,
  p_val_threshold = 1e-04,
  out_folder = "gen3DNet",
  verbose = TRUE
)

Arguments

left	Matrix of left objects
right	Matrix of right objects
nmf_nrun	Number of iterations to use for NMF
k	Number of clusters to use for NMF. This can be specified as a single number, or consecutive range. If unspecified, k is picked from 1 to min(num_cols - 1, num_rows - 1)
k_picker	Method for picking k. If unspecified, k values are compared using the KL-index of Ward clusterings based on euclidean distance. Possible values: max_cophenetic kneedle_silhouette_consensus kneedle_cophenetic max_silhouette_consensus max_cophenetic max_ward_kl To learn more, use help() for each of these functions.
seed	Seed to use for NMF.
p_val_threshold	Threshold for significant p-values in PLSR.
out_folder	Folder used for outputting results.
verbose	Whether to print output (default TRUE).

Examples

library("gen3DNet")
histon_path <- system.file("extdata", "histon_data.csv", package="gen3DNet")
phospho_path <- system.file("extdata", "phospho_data.csv", package="gen3DNet")
result <- gen3DNet(
   histon_path,
   phospho_path,
   nmf_nrun = 10,
   p_val_threshold = 0.01, 
   # k_picker = max_cophenetic
   # k_picker = kneedle_silhouette_consensus
   # k_picker = kneedle_cophenetic 
   # k_picker = max_silhouette_consensus
   # k_picker = max_cophenetic
   # k_picker = max_ward_kl
   k_picker = max_ward_kl
)

MollahLab/gen3DNet documentation built on Nov. 18, 2024, 5:08 a.m.