mp_filter_taxa-methods: Filter OTU (Features) By Abundance Level

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

Filter OTU (Features) By Abundance Level

Description

Filter OTU (Features) By Abundance Level

Usage

mp_filter_taxa(
  .data,
  .abundance = NULL,
  min.abun = 0,
  min.prop = 0.05,
  include.lowest = FALSE,
  ...
)

## S4 method for signature 'MPSE'
mp_filter_taxa(
  .data,
  .abundance = NULL,
  min.abun = 0,
  min.prop = 0.05,
  include.lowest = FALSE,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_filter_taxa(
  .data,
  .abundance = NULL,
  min.abun = 0,
  min.prop = 0.05,
  include.lowest = FALSE,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_filter_taxa(
  .data,
  .abundance = NULL,
  min.abun = 0,
  min.prop = 0.05,
  include.lowest = FALSE,
  ...
)

Arguments

.data	MPSE or tbl_mpse or grouped_df_mpse object.
.abundance	the column names of abundance, default is NULL, meaning the 'Abundance' column.
min.abun	numeric minimum abundance required for each one sample default is 0 (.abundance=Abundance or NULL), meaning the abundance of OTU (Features) for each one sample should be >= 0.
min.prop	numeric minimum proportion of samples that contains the OTU (Features) when min.prop larger than 1, meaning the minimum number of samples that contains the OTU (Features).
include.lowest	logical whether include the lower boundary of min.abun default is FALSE ( > min.abun), if it is TRUE, meaning (>= min.abun).
...	additional parameters, meaningless now.

Author(s)

Shuangbin Xu

Examples

data(mouse.time.mpse)
mouse.time.mpse %>% mp_filter_taxa(.abundance=Abundance, min.abun=1, min.prop=1)
# For tbl_mpse object.
mouse.time.mpse %>% as_tibble %>% mp_filter_taxa(.abundance=Abundance, min.abun=1, min.prop=1)
# This also can be done using group_by, filter of dplyr.
mouse.time.mpse %>% 
 dplyr::group_by(OTU) %>% 
 dplyr::filter(sum(Abundance>=1)>=1)

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