Can I adjust p value in correlation-based network analysis?

[rainboy352900]

Hi Liu,

I'm wondering whether I can adjust p value in correlation-based network analysis? Such as using false discovery rate method. I did not find the related function in trans_network$new.

Thanks.

[ChiLiubio]

Hi @rainboy352900
It is in the cal_network function COR_p_adjust parameter.

Chi

[rainboy352900]

Hi Chi,

Sorry to bother you again.

In your FEMS Microbiology Ecology paper, Figure 5b was generated by "cal_sum_links", but I do not find it in v0.10.1. Is there any alternative function available?

Thanks.

[ChiLiubio]

Hi @rainboy352900
Please see the mecodev package part of the tutorial. I moved this part to trans_netchord class in mecodev package since I think this part is not so important as other functions. But now I find many are interested in this chord plot. So I decide to move back this to microeco package in the coming v0.11.0 :)

Chi

[rainboy352900]

Thanks Chi.

I came across an error when running "trans_netchord$new" function in "mecodev" package. The example data seems ok. Cound you please suggest how to deal with it? Thanks.

library(microeco)
library(mecodev)
data<- read.csv(file="otu.csv",header=T, row.names=1)
taxonomy_table_16S<- read.csv(file="taxonomy.csv",header=T, row.names=1)
dataset <- microtable$new(otu_table = data, tax_table = taxonomy_table_16S)
t1 <- trans_network$new(dataset = dataset, cal_cor = "base", taxa_level = "OTU", filter_thres = 0, cor_method = "spearman")
t1$cal_network(COR_p_thres = 0.05, COR_p_adjust = "fdr", COR_optimization = TRUE)
test1 <- trans_netchord$new(dataset = t1, taxa_level = "Phylum")

otu.csv
taxonomy.csv

[ChiLiubio]

Hi @rainboy352900

I test all the steps and do not get the error. The microeco version I use is v0.10.1. Please check your version and try again.

[rainboy352900]

Thanks Chi. I'll try it again.