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

mp_extract_abundanceR Documentation

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


xiangpin/MicrobiotaProcess documentation built on July 24, 2024, 11:44 p.m.