bs_pm-mina: Inferring the network of different group of samples and test...

In Guan06/mina: Microbial community dIversity and Network Analysis

Description

Inferring the network of different group of samples and test significance by permutation.

Usage

## S4 method for signature 'mina,ANY'
bs_pm(
  x,
  group,
  g_size = 88,
  s_size = 30,
  rm = TRUE,
  per = 0.1,
  sig = TRUE,
  bs = 6,
  pm = 6,
  individual = FALSE,
  out_dir = "./",
  ...
)

## S4 method for signature 'mina,character'
bs_pm(
  x,
  group,
  g_size = 88,
  s_size = 30,
  rm = TRUE,
  per = 0.1,
  sig = TRUE,
  bs = 6,
  pm = 6,
  individual = FALSE,
  out_dir = "./",
  ...
)

Arguments

x	An object of class 'mina' with @norm and @des defined.
group	The column name of descriptive file @des for comparison.
g_size	The cutoff of group size used for filtering, default is 88.
s_size	The number of samples used for network inference during bootstrap and permutation (when 'sig' is TRUE), it should be smaller than g_size / 2 to make sure the randomness; default is 30.
rm	Filtering the components present in less than 'per' of the samples from compared groups, default TRUE.
per	The percentage of present samples for filtering, default is 0.1.
sig	Whether to test the significance, skip the permutation when set as FALSE, default is TRUE.
bs	The times for bootstrap network inference, default is 6.
pm	The times for permuatated samples network inference, default is 6.
individual	Whether to output the bootstrap and permutation results of each comparison individually, default is FALSE.
out_dir	The output directory if 'individual' is TRUE, default is the current working directory
...	Additional parameters.

Value

x The same object with @multi and @perm defined.

Examples

maize <- new("mina", tab = maize_asv2, des = maize_des2)
maize <- norm_tab(maize, method = "raref")
maize <- fit_tabs(maize)
maize <- bs_pm(maize, group = "Compartment", per = 0.5)

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