Apply all harmonization methods to a precision object

This function applies all harmonization methods to the raw data contained in a precision object. The harmonization results are added to the corresponding slots in the object for each dataset ("train", "test1", "test2") if they exist.

Usage

harmon.all(object, add.raw = TRUE)

Arguments

object

A precision object containing raw data. Harmonization is applied to the slots raw.train.data, raw.test1.data, and raw.test2.data (if applicable), each containing a list with data and label elements.

add.raw

Logical. If TRUE, add the raw data to the harmonized data

Value

A precision object with harmonization results added to the slots harmon.train.data, harmon.test1.data, and harmon.test2.data (if applicable).

Details

The following harmonization methods are applied to the data:

• No Harmonization (if add.raw = TRUE)

• Total Count (TC) (harmon.TC)

• Upper Quartile (UQ) (harmon.UQ)

• Median (median) (harmon.med)

• Trimmed Median of Means (TMM) (harmon.TMM)

• DESeq (harmon.DESeq)

• PoissonSeq (harmon.PoissonSeq)

• Quantile Normalization (QN) (harmon.QN)

• Remove Unwanted Variation (RUVg, RUVr, and RUVs) (harmon.RUVg), (harmon.RUVr), (harmon.RUVs)