abundances-methods: Extract taxa abundances

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

Extract taxa abundances

Description

Extract taxa abundances from phyloseq objects.

Usage

abundances(object, transform = c("identity", "log10", "log10p"), norm = FALSE)

## S4 method for signature 'otu_table'
abundances(object, transform = c("identity", "log10", "log10p"), norm = FALSE)

## S4 method for signature 'phyloseq'
abundances(object, transform = c("identity", "log10", "log10p"), norm = FALSE)

## S4 method for signature 'microbiomeMarker'
abundances(object, transform = c("identity", "log10", "log10p"))

Arguments

object	otu_table, phyloseq, or microbiomeMarker.
transform	transformation to apply, the options inclulde: "identity", return the original data without any transformation. "log10", the transformation is log10(object), and if the data contains zeros the transformation is log10(1 + object). "log10p", the transformation is log10(1 + object).
norm	logical, indicating whether or not to return the normalized taxa abundances.

Value

abundance matrix with taxa in rows and samples in columns.

See Also

otu_table, phyloseq, microbiomeMarker,transform_abundances

Examples

data(caporaso)
abd <- abundances(caporaso)

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.