get_alltaxadf: get the table of abundance of all level taxonomy

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

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",
  include.rownames = FALSE,
  ...
)

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

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.
include.rownames	logical whether to calculate the original feature data, default is FALSE.
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

## Not run: 
   data(test_otu_data)
   alltaxatab <- get_alltaxadf(test_otu_data)
   head(alltaxatab[,1:10])

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.