transform_abundances: Transform the taxa abundances in 'otu_table' sample by sample

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

Transform the taxa abundances in otu_table sample by sample

Description

Transform the taxa abundances in otu_table sample by sample, which means the counts of each sample will be transformed individually.

Usage

transform_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).

Value

A object matches the class of argument object with the transformed otu_table.

See Also

abundances()

Examples

data(oxygen)
x1 <- transform_abundances(oxygen)
head(otu_table(x1), 10)
x2 <- transform_abundances(oxygen, "log10")
head(otu_table(x2), 10)
x3 <- transform_abundances(oxygen, "log10p")
head(otu_table(x3), 10)

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