corBiostripe: Inter-Domain Ecological Network, we call this biostripe...

In taowenmicro/ggClusterNet:

Inter-Domain Ecological Network, we call this biostripe network

Description

Inter-Domain Ecological Network, we call this biostripe network

Usage

corBiostripe(
  data = NULL,
  group = NULL,
  ps = NULL,
  r.threshold = 0.6,
  p.threshold = 0.05,
  method = "spearman"
)

Arguments

ps	phyloseq Object, contains OTU tables, tax table and map table, represented sequences,phylogenetic tree.
r.threshold	The defult, r.threshold=0.6, it represents the correlation that the absolute value of the correlation threshold is greater than 0.6. the value range of correlation threshold from 0 to 1.
p.threshold	The defult, p.threshold=0.05, it represents significance threshold below 0.05.
method	method for Correlation calculation,method="pearson" is the default value. The alternatives to be passed to cor are "spearman" and "kendall".
N	filter OTU tables by abundance.The defult, N=0.02, extract the top 0.02 relative abundance of OTU.

Value

list which contains OTU correlation matrix

Author(s)

Contact: Tao Wen [e-mail] Penghao Xie [e-mail] yongxin liu [e-mail] Jun Yuan [e-mail]

References

Tao Wen#, Penghao Xie#, Shengdie Yang, Guoqing Niu, Xiaoyu Liu, Zhexu Ding, Chao Xue, Yong-Xin Liu *, Qirong Shen, Jun Yuan* ggClusterNet: an R package for microbiome network analysis and modularity-based multiple network layouts iMeta 2022,DOI: doi: 10.1002/imt2.32

Examples

data(ps)
result <- corMicro(ps = ps,N = 0.02,r.threshold=0.6,p.threshold=0.05,method = "pearson")
# extract cor matrix
cor = result[[1]]

taowenmicro/ggClusterNet documentation built on March 29, 2025, 1:04 p.m.