perSampleDominantTaxa {mia}R Documentation

Get dominant taxa

Description

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

Usage

perSampleDominantTaxa(x, abund_values = "counts", rank = NULL, ...)

## S4 method for signature 'SummarizedExperiment'
perSampleDominantTaxa(x, abund_values = "counts", rank = NULL, ...)

addPerSampleDominantTaxa(x, name = "dominant_taxa", ...)

## S4 method for signature 'SummarizedExperiment'
addPerSampleDominantTaxa(x, name = "dominant_taxa", ...)

Arguments

x

A SummarizedExperiment object.

abund_values

A single character value for selecting the assay to use for identifying dominant taxa.

rank

A single character defining a taxonomic rank. Must be a value of the output of taxonomicRanks().

...

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 addPerSampleDominantTaxa.

Details

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

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

perSampleDominantTaxa returns a named character vector x while addPerSampleDominantTaxa 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 <- perSampleDominantTaxa(x, rank="Genus")

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

[Package mia version 1.2.7 Index]