extractVarPart {variancePartition} | R Documentation

## Extract variance statistics

### Description

Extract variance statistics from list of models fit with `lm()` or `lmer()`

### Usage

    extractVarPart(modelList, showWarnings = TRUE, ...)

### Arguments

`modelList` | list of `lmer()` model fits
`showWarnings` | show warnings about model fit (default TRUE)
`...` | other arguments

### Value

`data.frame` of fraction of variance explained by each variable, after correcting for all others.

### Examples

    # 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)

    # Step 1: fit linear mixed model on gene expresson
    # If categoritical variables are specified, a linear mixed model is used
    # If all variables are modeled as continuous, a linear model is used
    # each entry in results is a regression model fit on a single gene
    # Step 2: extract variance fractions from each model fit
    # for each gene, returns fraction of variation attributable to each variable
    # Interpretation: the variance explained by each variable
    # after correction for all other variables
    varPart <- fitExtractVarPartModel( geneExpr, form, info )

    # violin plot of contribution of each variable to total variance
    plotVarPart( sortCols( varPart ) )

    # Advanced:
    # Fit model and extract variance in two separate steps
    # Step 1: fit model for each gene, store model fit for each gene in a list
    results <- fitVarPartModel( geneExpr, form, info )

    # Step 2: extract variance fractions
    varPart <- extractVarPart( results )

[Package variancePartition version 1.20.0 Index]