get_net_cls_tab {mina}R Documentation

Get the cluster table 'cls_tab' from quantitative table 'norm' and network clustering results 'cls'.

Description

Get the cluster table 'cls_tab' from quantitative table 'norm' and network clustering results 'cls'.

Usage

get_net_cls_tab(x_norm, x_cls, uw = FALSE)

Arguments

x_norm

The normalized quantitative table used for netowrk inference and clustering.

x_cls

The network clustering table.

uw

By summing up the number of present components of each cluster instead of relative abundance, default is FALSE.

Value

x_cls The quantitative table with clusters in rows.

Examples

maize <- new("mina", tab = maize_asv2, des = maize_des2)
maize <- norm_tab(maize, method = "raref", depth = 1000)
maize <- fit_tabs(maize)
maize_norm <- norm(maize)
maize_adj <- adj(maize_norm, method = "spearman")
maize_cls <- net_cls(maize_adj, method = "ap", cutoff = 0.5)
maize_cls_tab <- get_net_cls_tab(maize_norm, maize_cls)

[Package mina version 1.2.0 Index]