constructingNetwork: Getting gene lineage from score matrix.

In Busydog1990/genepro: CProtMEDIAS: clustering of amino acid sequences encoded by gene families by MErging and DIgitizing Aligned Sequences

Getting gene lineage from score matrix.

Description

Getting gene lineage from score matrix.

Usage

constructingNetwork(
  data,
  range = NULL,
  thresh = 0.1,
  normalization = T,
  group = NULL,
  alpha = 0.01,
  theta1 = 0.8,
  rootNode = 1
)

Arguments

data	Matrix. Score matrix of each site.
range	Numeric. Extract the specified column of the score matrix for network construction.
thresh	Numeric. Edges whose correlation is less than thresh will be filtered out.
normalization	Logical. To normalize the data or not. Default:TRUE.
group	Factor. Grouping information of each gene. Must contain the same length of nrow(data).
alpha	significance level for a two-sided Wilcoxon rank-sum test of the distribution of scEnergy between two metagenes.Default:0.01.
theta1	Numeric. Select the genes which include theta1 energy in each cluster. Default:0.8.
rootNode	Numeric. The root node (i.e., start state) for inferring gene family lineages.

Value

a struct giving the gene lineage information.

Busydog1990/genepro documentation built on July 20, 2023, 6:03 a.m.