getDominant: Get dominant taxa

In FelixErnst/mia: Microbiome analysis

Get dominant taxa

Description

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

Usage

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

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

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

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

Arguments

x	TreeSummarizedExperiment.
assay.type	Character scalar. Specifies which assay to use for calculation. (Default: "counts")
assay_name	Deprecated. Use assay.type instead.
group	Character scalar. Defines a group. Must be one of the columns from rowData(x). (Default: NULL)
rank	Deprecated. Use group instead.
other.name	Character scalar. A name for features that are not included in n the most frequent dominant features in the data. (Default: "Other")
n	Numeric scalar. The number of features that are the most frequent dominant features. Default is NULL, which defaults that each sample is assigned a dominant taxon. (Default: NULL)
complete	Logical scalar. A value to manage multiple dominant taxa for a sample. Default for getDominant is TRUE to include all equally dominant taxa for each sample. complete = FALSE samples one taxa for the samples that have multiple. Default for addDominant 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	Character scalar. A name for the column of the colData where results will be stored. (Default: "dominant_taxa")

Details

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

With group parameter, it is possible to agglomerate rows based on groups. If the value is one of the columns in taxonomyRanks(), agglomerateByRank() is applied. Otherwise, agglomerateByVariable() is utilized. E.g. if 'Genus' rank is used, all abundances of same Genus are added together, and agglomerated features are returned. See corresponding functions for additional arguments to deal with missing values or special characters.

Value

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

Examples

data(GlobalPatterns)
x <- GlobalPatterns

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

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

FelixErnst/mia documentation built on Nov. 18, 2024, 5:02 a.m.