cor_Big_micro2: Correlation network calculation of big microbial community...

In taowenmicro/ggClusterNet:

Correlation network calculation of big microbial community data

Description

Correlation network calculation of big microbial community data

Usage

cor_Big_micro2(
  ps = ps,
  N = 0,
  p.threshold = 0.05,
  r.threshold = 0.9,
  scale = FALSE,
  method = "spearman",
  met.scale = "TMM",
  p.adj = "BH"
)

Arguments

ps	phyloseq Object, contains OTU tables, tax table and map table, represented sequences,phylogenetic tree.
N	filter OTU tables by abundance.The defult, N=0, extract the top N number relative abundance of OTU.
p.threshold	The defult, p.threshold=0.05, it represents significance threshold below 0.05.
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.
scale	Whether to standardize microbiome data; TRUE or FALSE need selected.
method	method for Correlation calculation,method="pearson" is the default value. The alternatives to be passed to cor are "spearman" and "kendall".
met.scale	Microbiome data normalization methods; could be selected by rela, sampling, log,TMM,RLE,upperquartile et al
p.adj	A vector of character strings containing the names of the multiple testing procedures for which adjusted p-values are to be computed. This vector should include any of the following: "Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BH", "BY", "ABH", "TSBH".

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 <- cor_Big_micro(ps = ps,N = 0,p.threshold = 0.05,r.threshold = 0.9,scale = FALSE)
# extract cor matrix
cor = result[[1]]

taowenmicro/ggClusterNet documentation built on March 29, 2024, 1:32 a.m.