corMicro | R Documentation |
Correlation network calculation of microbial community data
corMicro(
ps = ps,
N = 0,
r.threshold = 0.6,
method.scale = "rela",
p.threshold = 0.05,
method = "pearson",
R = 10,
ncpus = 1
)
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. |
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. |
method.scale |
sacleing method for microbiome data, rela, log,TMM,RLC··· |
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". recentliy "sparcc" added to method |
R |
number of repeats for sparcc p value |
ncpus |
number of cpu for sparcc calculate p value |
list which contains OTU correlation matrix
Contact: Tao Wen taowen@njau.edu.cn Penghao Xie 2019103106@njau.edu.cn yongxin liu yxliu@genetics.ac.cn Jun Yuan junyuan@njau.edu.cn
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
data(ps)
result <- corMicro(ps = ps,N = 100,r.threshold=0.6,p.threshold=0.05,method = "pearson")
# extract cor matrix
cor = result[[1]]
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