mp_extract_abundance-methods: Extracting the abundance metric from MPSE or tbl_mpse object

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

Extracting the abundance metric from MPSE or tbl_mpse object

Description

Extracting the abundance metric from the MPSE or tbl_mpse, the 'mp_cal_abundance' must have been run with action='add'.

Usage

mp_extract_abundance(x, taxa.class = "all", topn = NULL, rmun = FALSE, ...)

## S4 method for signature 'MPSE'
mp_extract_abundance(x, taxa.class = "all", topn = NULL, rmun = FALSE, ...)

## S4 method for signature 'tbl_mpse'
mp_extract_abundance(x, taxa.class = "all", topn = NULL, rmun = FALSE, ...)

## S4 method for signature 'grouped_df_mpse'
mp_extract_abundance(x, taxa.class = "all", topn = NULL, rmun = FALSE, ...)

Arguments

x	MPSE or tbl_mpse object
taxa.class	character the name of taxonomy class level what you want to extract
topn	integer the number of the top most abundant, default is NULL.
rmun	logical whether to remove the unknown taxa, such as "g__un_xxx", default is FALSE (the unknown taxa class will be considered as 'Others').
...	additional parameters

Author(s)

Shuangbin Xu

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