mp_filter_taxa {MicrobiotaProcess} | R Documentation

## 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)

[Package MicrobiotaProcess version 1.4.4 Index]