bs_pm,mina,ANY-method {mina} | R Documentation

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

### 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)

[Package mina version 1.2.0 Index]