get_alltaxadf {MicrobiotaProcess} | R Documentation

## get the table of abundance of all level taxonomy

### Description

This function was designed to get the abundance of all level taxonomy, the input can be phyloseq object or data.frame.

### Usage

    get_alltaxadf(obj, ...)

    ## S4 method for signature 'phyloseq'
    get_alltaxadf(obj, method = NULL, type = "species", ...)

    ## S4 method for signature 'data.frame'
    get_alltaxadf(
      obj,
      taxda,
      taxa_are_rows = FALSE,
      method = NULL,
      type = "species",
      ...
    )

### Arguments

`obj` | object, phyloseq or data.frame
`...,` | additional parameters, see also `decostand`.
`method` | character, the normalization method, see also `decostand`, default is NULL, the relative abundance will be return, if it set 'count', the count table will be return.
`taxda` | data.frame, the taxonomy table.
`taxa_are_rows` | logical, if the obj is data.frame, and the features are rownames, the taxa_are_rows should be set TRUE, default FALSE, meaning the features are colnames.

### Value

the all taxonomy abundance table

### Author(s)

Shuangbin Xu

### Examples

    data(test_otu_data)
    alltaxatab <- get_alltaxadf(test_otu_data)
    head(alltaxatab[,1:10])

[Package MicrobiotaProcess version 1.2.2 Index]