net_dis_indi: Calculate the network distance of bootstrap and permutation...

In Guan06/mina: Microbial community dIversity and Network Analysis

Description

Calculate the network distance of bootstrap and permutation when appliable.

Calculate the network distance of bootstrap and permutation when appliable.

Usage

net_dis_indi(x, method, ...)

## S4 method for signature 'character,ANY'
net_dis_indi(
  x,
  method,
  evk = 100,
  sig = TRUE,
  skip = TRUE,
  egv = TRUE,
  dir = "./",
  ...
)

## S4 method for signature 'character,character'
net_dis_indi(
  x,
  method,
  evk = 100,
  sig = TRUE,
  skip = TRUE,
  egv = TRUE,
  dir = "./",
  ...
)

Arguments

x	The folder store the network inference results. defined.
method	The distance to be calculated, "spectra" and "Jaccard" are available.
...	Additional parameters.
evk	The first 'evk' eigenvalues will be used for 'spectra' distance, the default is 100.
sig	Whether to test the significance, if TRUE (by default), permutation results should be included in the folder 'x'.
skip	Whether to skip the comparison when the dimenstion of adjacency matrix is smaller than setted 'evk', default TRUE.
egv	Wheather to output the eigenvectors for Spectral distance, the defult is TRUE, only validate when 'method == "spectra"'.
dir	The folder to output the eigenvectors, only validate when 'egv == TRUE'.

Value

y The 'mina' object with 'dis_bs', 'dis_pm' and 'dis_stat'.

y The 'mina' object with 'dis_bs', 'dis_pm' and 'dis_stat'.

Examples

## Not run: 
data(maize)
maize <- norm_tab(maize, method = "raref")
maize <- fit_tabs(maize)
maize <- get_rep(maize, top = 5)
maize <- bs_pm(maize, group = "Compartment", individual = TRUE, out_dir =
"./individual_bs_pm/")
maize_stat1 <- net_dis_indi(x = "./individual_bs_pm/", method = "spectra")
maize_stat2 <- net_dis_indi(x = "./individual_bs_pm/", method = "Jaccard")
maize_stat3 <- net_dis_indi(x = "./individual_bs_pm/", method = "spectra",
evk = 100, skip = TRUE)

## End(Not run)
## Not run: 
data(maize)
norm(maize) <- maize_asv2
maize <- fit_tabs(maize)
maize <- get_rep(maize, top= 5)
maize <- bs_pm(maize, group = "Compartment", individual = TRUE, out_dir =
"./individual_bs_pm/")
maize_stat1 <- net_dis_indi("./individual_bs_pm/", method = "spectra")
maize_stat2 <- net_dis_indi("./individual_bs_pm/", method = "Jaccard")
maize_stat3 <- net_dis_indi("./individual_bs_pm/", method = "spectra",
evk = 100, skip = TRUE)

## End(Not run)

Guan06/mina documentation built on Feb. 21, 2022, 11:56 a.m.