residuals-VarParFitList-method: Residuals from model fit

In variancePartition: Quantify and interpret divers of variation in multilevel gene expression experiments

Description

Extract residuals for each gene from model fit with fitVarPartModel()

Usage

## S4 method for signature 'VarParFitList'
residuals(object, ...)

Arguments

object	object produced by fitVarPartModel()
...	other arguments.

Details

If model is fit with missing data, residuals returns NA for entries that were missing in the original data

Value

Residuals extracted from model fits stored in object

Examples

# load library
# library(variancePartition)

# Intialize parallel backend with 4 cores
library(BiocParallel)
register(SnowParam(4))

# load simulated data:
# geneExpr: matrix of gene expression values
# info: information/metadata about each sample
data(varPartData)

# Specify variables to consider
# Age is continuous so we model it as a fixed effect
# Individual and Tissue are both categorical, so we model them as random effects
form <- ~ Age + (1|Individual) + (1|Tissue) 

# Fit model
modelFit <- fitVarPartModel( geneExpr, form, info )

# Extract residuals of model fit
res <- residuals( modelFit )

variancePartition documentation built on Nov. 8, 2020, 5:18 p.m.