computeANOVA: Anova test for batch effect on individual gene expressions
In AbhishekSinha28/tcgaCleaneR: TGCA Data Analysis

computeANOVA

R Documentation

Anova test for batch effect on individual gene expressions

Description

This function is a part of the data analysis functionality of tcgaCleaneR. It use ANOVA F statistics to summarize the effects of a qualitative source of unwanted variation (e.g. batches) on the expression levels of individual genes. Unwanted Variations such as Plate effect and Time effect can be analysed by this test.

Usage

computeANOVA(data, variable, is.log, n.cores)

Arguments

`data`	S4 data object
`variable`	character: The predictor variable to `lm` model. The variables included are 'Time' and 'Plate'
`is.log`	logical: Checks if the S4 data has log values. It 'False', it converts data to log scale.
`n.cores`	The number of cores to use, i.e. at most how many child processes will be run simultaneously. Must be at least one, and parallel computing requires at least two cores.

Value

A S3 data frame. The output contains the Anova test (F test) scores corresponding to all genes in S4 data object.

Examples

## Not run: 
computeANOVA(data = brca.data, variable = "Time", is.log = FALSE, n.cores = 1)
computeANOVA(data = brca.data, variable = "Plate", is.log = FALSE, n.cores = 1)

## End(Not run)

AbhishekSinha28/tcgaCleaneR documentation built on May 6, 2022, 6:46 a.m.