networks_taxa_role: networks_taxa_role

In lindan1128/coreMicrobiome: Core microbiome analysis and visualization

networks_taxa_role

Description

Determine the role of the taxa in a network.

Usage

networks_taxa_role(
  otu,
  taxa,
  sample,
  pre_threshold,
  fdr_threshold,
  cor_threshold,
  permutation,
  cluster_method,
  propr = TRUE,
  sparcc = TRUE,
  cclasso = TRUE
)

Arguments

otu	a community count data matrix with samples in rows and OTUs/taxa in column,
taxa	a taxa information matrix. The rownames must match the OTU names (taxa_names) of the otu,
sample	a sample information data.frame. The rownames must match the sample names in the otu,
pre_threshold	occurrence frequency,
fdr_threshold	fdr threshold,
cor_threshold	association threshold,
permutation	permutation number of the association methods,
cluster_method	module clustering methods, including cluster_walktrap, cluster_edge_betweenness, cluster_fast_greedy and cluster_spinglass,
propr	a logical value indicating whether to run propr,
sparcc	a logical value indicating whether to run sparcc,
cclasso	a logical value indicating whether to run cclasso,

Details

Determine the role of the taxa in a network.

Value

A dataframe containing the role of the taxa in a network.

Examples

 networks_taxa_role(otu, taxa, sample, pre_threshold=0.5, fdr_threshold=0.1, cor_threshold=0.6, permutation=100, cluster_method="cluster_walktrap", propr=TRUE, sparcc=TRUE, cclasso=TRUE)

lindan1128/coreMicrobiome documentation built on May 5, 2022, 8:24 p.m.