run_transform: Transform the expression profile in 'assayData' sample by...

In HuaZou/MyRtools: Statistic Approaches on Data Analysis

Description

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

Usage

run_transform(object, transform=c("none", "log2", "log2p", "log10", "log10p"))

Arguments

object,	Object; a ['matrix'] or ['assayData-class'] or ['ExpressionSet-class'].
transform,	Character; transformation to apply, the options inclulde: * "none": return the original data without any transformation. * "log2" or "log10": the transformation is 'log2(object)' or 'log10(object)', and if the data contains zeros the transformation is 'log2(1 + object)' or 'log10(1 + object)'. * "log2p" or "log10p": the transformation is 'log2(1 + object)' or 'log10(1 + object)'.

Value

A object matches the class of argument 'object' with the transformed profile matrix.

References

https://github.com/yiluheihei/microbiomeMarker.

HuaZou/MyRtools documentation built on Jan. 6, 2022, 8:56 a.m.