mp_stat_taxa-methods: Count the number and total number taxa for each sample at...

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

Count the number and total number taxa for each sample at different taxonomy levels

Description

Count the number and total number taxa for each sample at different taxonomy levels

Usage

mp_stat_taxa(.data, .abundance, action = "add", ...)

## S4 method for signature 'MPSE'
mp_stat_taxa(.data, .abundance, action = "add", ...)

## S4 method for signature 'tbl_mpse'
mp_stat_taxa(.data, .abundance, action = "add", ...)

## S4 method for signature 'grouped_df_mpse'
mp_stat_taxa(.data, .abundance, action = "add", ...)

Arguments

.data	MPSE or tbl_mpse object
.abundance	the column name of abundance to be calculated
action	a character "get" returns a table only contained the number and total number for each sample at different taxonomy levels, "only" returns a non-redundant tibble contained a nest column (StatTaxaInfo) and other sample information, "add" returns a update object (.data) contained a nest column (StatTaxaInfo).
...	additional parameter

Value

update object or tbl_df according action argument

Author(s)

Shuangbin Xu

Examples

data(mouse.time.mpse)
mouse.time.mpse %>%
 mp_stat_taxa(.abundance=Abundance, action="only")

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