TCGAbatch_Correction: Batch correction using ComBat and Voom transformation using...

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Batch correction using ComBat and Voom transformation using limma package.

Description

TCGAbatch_correction allows user to perform a Voom correction on gene expression data and have it ready for DEA. One can also use ComBat for batch correction for exploratory analysis. If batch.factor or adjustment argument is "Year" please provide clinical data. If no batch factor is provided, the data will be voom corrected only

TCGAanalyze_DEA performs DEA using following functions from sva and limma:

1. limma::voom Transform RNA-Seq Data Ready for Linear Modelling.

2. sva::ComBat Adjust for batch effects using an empirical Bayes framework.

Usage

TCGAbatch_Correction(
  tabDF,
  batch.factor = NULL,
  adjustment = NULL,
  ClinicalDF = data.frame(),
  UnpublishedData = FALSE,
  AnnotationDF = data.frame()
)

Arguments

tabDF	numeric matrix, each row represents a gene, each column represents a sample
batch.factor	a string containing the batch factor to use for correction. Options are "Plate", "TSS", "Year", "Portion", "Center"
adjustment	vector containing strings for factors to adjust for using ComBat. Options are "Plate", "TSS", "Year", "Portion", "Center"
ClinicalDF	a dataframe returned by GDCquery_clinic() to be used to extract year data
UnpublishedData	if TRUE perform a batch correction after adding new data
AnnotationDF	a dataframe with column Batch indicating different batches of the samples in the tabDF

Value

data frame with ComBat batch correction applied

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.