summaries {mia} | R Documentation

## Summarizing microbiome data

### Description

To query a `SummarizedExperiment` for interesting features, several functions are available.

### Usage

    getTopTaxa(
      x,
      top = 5L,
      method = c("mean", "sum", "median"),
      abund_values = "counts"
    )

    ## S4 method for signature 'SummarizedExperiment'
    getTopTaxa(
      x,
      top = 5L,
      method = c("mean", "sum", "median", "prevalence"),
      abund_values = "counts"
    )

    getUniqueTaxa(x, ...)

    ## S4 method for signature 'SummarizedExperiment'
    getUniqueTaxa(x, rank = NULL)

    countDominantTaxa(x, group = NULL, ...)

    ## S4 method for signature 'SummarizedExperiment'
    countDominantTaxa(x, group = NULL, ...)

    ## S4 method for signature 'SummarizedExperiment'
    summary(object, abund_values = "counts")

### Arguments

`x` | A `SummarizedExperiment` object.
`top` | Numeric value, how many top taxa to return. Default return top five taxa.
`method` | Specify the method to determine top taxa. Either sum, mean, median or prevalence. Default is 'mean'.
`abund_values` | a `character` value to select an `assayNames` By default it expects count data.
`...` | Additional arguments passed on to `agglomerateByRank()` when `rank` is specified for `countDominantTaxa`.
`rank` | A single character defining a taxonomic rank. Must be a value of the output of `taxonomicRanks()`.
`group` | With group, it is possible to group the observations in an overview. Must be one of the column names of `colData`.
`object` | A `SummarizedExperiment` object.

### Details

The `getTopTaxa` extracts the most `top` abundant “FeatureID”s in a `SummarizedExperiment` object.

The `getUniqueTaxa` is a basic function to access different taxa at a particular taxonomic rank.

`countDominantTaxa` returns information about most dominant taxa in a tibble. Information includes their absolute and relative abundances in whole data set.

The `summary` will return a summary of counts for all samples and features in `SummarizedExperiment` object.

### Value

The `getTopTaxa` returns a vector of the most `top` abundant “FeatureID”s

The `getUniqueTaxa` returns a vector of unique taxa present at a particular rank

The `countDominantTaxa` returns an overview in a tibble. It contains dominant taxa in a column named `*name*` and its abundance in the data set.

The `summary` returns a list with two `tibble`s

### Author(s)

Leo Lahti, Tuomas Borman and Sudarshan A. Shetty

### See Also

`getPrevalentTaxa`

`perCellQCMetrics`, `perFeatureQCMetrics`, `addPerCellQC`, `addPerFeatureQC`, `quickPerCellQC`

### Examples

    data(GlobalPatterns)
    top_taxa <- getTopTaxa(GlobalPatterns,
                           method = "mean",
                           top = 5,
                           abund_values = "counts")
    top_taxa

    # Gets the overview of dominant taxa
    dominant_taxa <- countDominantTaxa(GlobalPatterns,
                                       rank = "Genus")
    dominant_taxa

    # With group, it is possible to group observations based on specified groups
    # Gets the overview of dominant taxa
    dominant_taxa <- countDominantTaxa(GlobalPatterns,
                                       rank = "Genus",
                                       group = "SampleType",
                                       na.rm= TRUE)

    dominant_taxa

    # Get an overview of sample and taxa counts
    summary(GlobalPatterns)

    # Get unique taxa at a particular taxonomic rank
    getUniqueTaxa(GlobalPatterns, "Phylum")

[Package mia version 1.2.7 Index]