perSampleDominantTaxa: Get dominant taxa

In microbiome/mia: Microbiome analysis

Get dominant taxa

Description

These functions return information about the most dominant taxa in a SummarizedExperiment object.

Usage

perSampleDominantFeatures(
  x,
  assay.type = assay_name,
  assay_name = "counts",
  rank = NULL,
  other.name = "Other",
  n = NULL,
  complete = TRUE,
  ...
)

## S4 method for signature 'SummarizedExperiment'
perSampleDominantFeatures(
  x,
  assay.type = assay_name,
  assay_name = "counts",
  rank = NULL,
  other.name = "Other",
  n = NULL,
  complete = TRUE,
  ...
)

perSampleDominantTaxa(x, ...)

## S4 method for signature 'SummarizedExperiment'
perSampleDominantTaxa(x, ...)

addPerSampleDominantFeatures(
  x,
  name = "dominant_taxa",
  other.name = "Other",
  n = NULL,
  ...
)

## S4 method for signature 'SummarizedExperiment'
addPerSampleDominantFeatures(
  x,
  name = "dominant_taxa",
  other.name = "Other",
  n = NULL,
  complete = FALSE,
  ...
)

addPerSampleDominantTaxa(x, ...)

## S4 method for signature 'SummarizedExperiment'
addPerSampleDominantTaxa(x, ...)

Arguments

x	A SummarizedExperiment object.
assay.type	A single character value for selecting the assay to use for identifying dominant taxa.
assay_name	a single character value for specifying which assay to use for calculation. (Please use assay.type instead. At some point assay_name will be disabled.)
rank	A single character defining a taxonomic rank. Must be a value of the output of taxonomyRanks().
other.name	A name for features that are not included in n the most frequent dominant features in the data. Default is "Other".
n	The number of features that are the most frequent dominant features. Default is NULL, which defaults that each sample is assigned a dominant taxon.
complete	A boolean value to manage multiple dominant taxa for a sample. Default for perSampleDominantTaxa is TRUE to include all equally dominant taxa for each sample. complete = FALSE samples one taxa for the samples that have multiple. Default for addPerSampleDominantTaxa is FALSE to add a column with only one dominant taxon assigned for each sample into colData. complete = TRUE adds a list that includes all dominant taxa for each sample into colData.
...	Additional arguments passed on to agglomerateByRank() when rank is specified.
name	A name for the column of the colData where the dominant taxa will be stored in when using addPerSampleDominantFeatures.

Details

addPerSampleDominantFeatures extracts the most abundant taxa in a SummarizedExperiment object, and stores the information in the colData. It is a wrapper for perSampleDominantFeatures.

With rank parameter, it is possible to agglomerate taxa based on taxonomic ranks. E.g. if 'Genus' rank is used, all abundances of same Genus are added together, and those families are returned. See agglomerateByRank() for additional arguments to deal with missing values or special characters.

Value

perSampleDominantFeatures returns a named character vector x while addPerSampleDominantFeatures returns SummarizedExperiment with additional column in colData named *name*.

Author(s)

Leo Lahti, Tuomas Borman and Sudarshan A. Shetty.

Examples

data(GlobalPatterns)
x <- GlobalPatterns

# Finds the dominant taxa.
sim.dom <- perSampleDominantFeatures(x, rank="Genus")

# Add information to colData
x <- addPerSampleDominantFeatures(x, rank = "Genus", name="dominant_genera")
colData(x)

microbiome/mia documentation built on April 27, 2024, 4:04 a.m.