variancePartition (version 1.2.5)

residuals,VarParFitList-method: Residuals from model fit

Description

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

Usage

"residuals"(object, ...)

Arguments

object

object produced by fitVarPartModel()

...

other arguments.

Value

Residuals extracted from model fits stored in object

Details

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

Examples

# load library
# library(variancePartition)

# optional step to run analysis in parallel on multicore machines
# Here, we used 4 threads
library(doParallel)
cl <- makeCluster(4)
registerDoParallel(cl)
# or by using the doSNOW package

# 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 )

# stop cluster
stopCluster(cl)