residuals,VarParFitList-method {variancePartition} | R Documentation

## Residuals from model fit

### 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)

    # 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 )

[Package variancePartition version 1.18.3 Index]