variancePartition (version 1.2.5)

fitExtractVarPartModel: Fit linear (mixed) model, report variance fractions

Description

Fit linear (mixed) model to estimate contribution of multiple sources of variation while simultaneously correcting for all other variables. Report fraction of variance attributable to each variable

Usage

fitExtractVarPartModel(exprObj, formula, data, REML = FALSE, useWeights = TRUE, weightsMatrix = NULL, adjust = NULL, adjustAll = FALSE, showWarnings = TRUE, control = lme4::lmerControl(calc.derivs = FALSE, check.rankX = "stop.deficient"), ...)
"fitExtractVarPartModel"(exprObj, formula, data, REML = FALSE, useWeights = TRUE, weightsMatrix = NULL, adjust = NULL, adjustAll = FALSE, showWarnings = TRUE, control = lme4::lmerControl(calc.derivs = FALSE, check.rankX = "stop.deficient"), ...)
"fitExtractVarPartModel"(exprObj, formula, data, REML = FALSE, useWeights = TRUE, weightsMatrix = NULL, adjust = NULL, adjustAll = FALSE, showWarnings = TRUE, control = lme4::lmerControl(calc.derivs = FALSE, check.rankX = "stop.deficient"), ...)
"fitExtractVarPartModel"(exprObj, formula, data, REML = FALSE, useWeights = TRUE, weightsMatrix = NULL, adjust = NULL, adjustAll = FALSE, showWarnings = TRUE, control = lme4::lmerControl(calc.derivs = FALSE, check.rankX = "stop.deficient"), ...)
"fitExtractVarPartModel"(exprObj, formula, data, REML = FALSE, useWeights = TRUE, weightsMatrix = NULL, adjust = NULL, adjustAll = FALSE, showWarnings = TRUE, control = lme4::lmerControl(calc.derivs = FALSE, check.rankX = "stop.deficient"), ...)

Arguments

exprObj

matrix of expression data (g genes x n samples), or ExpressionSet, or EList returned by voom() from the limma package

formula

specifies variables for the linear (mixed) model. Must only specify covariates, since the rows of exprObj are automatically used a a response. e.g.: ~ a + b + (1|c)

data

data.frame with columns corresponding to formula

REML

use restricted maximum likelihood to fit linear mixed model. default is FALSE. Strongly discourage against changing this option

useWeights

if TRUE, analysis uses heteroskedastic error estimates from voom(). Value is ignored unless exprObj is an EList() from voom() or weightsMatrix is specified

weightsMatrix

matrix the same dimension as exprObj with observation-level weights from voom(). Used only if useWeights is TRUE

adjust

remove variation from specified variables from the denominator. This computes the adjusted ICC with respect to the specified variables

adjustAll

adjust for all variables. This computes the adjusted ICC with respect to all variables. This overrides the previous argument, so all variables are include in adjust.

showWarnings

show warnings about model fit (default TRUE)

control

control settings for lmer()

...

Additional arguments for lmer() or lm()

Value

list() of where each entry is a model fit produced by lmer() or lm()

Details

A linear (mixed) model is fit for each gene in exprObj, using formula to specify variables in the regression. If categorical variables are modeled as random effects (as is recommended), then a linear mixed model us used. For example if formula is ~ a + b + (1|c), then to model is

fit <- lmer( exprObj[j,] ~ a + b + (1|c), data=data)

If there are no random effects, so formula is ~ a + b + c, a 'standard' linear model is used:

fit <- lm( exprObj[j,] ~ a + b + c, data=data)

In both cases, useWeights=TRUE causes weightsMatrix[j,] to be included as weights in the regression model.

Note: Fitting the model for 20,000 genes can be computationally intensive. To accelerate computation, models can be fit in parallel using foreach/dopar to run loops in parallel. Parallel processing must be enabled before calling this function. See below.

The regression model is fit for each gene separately. Samples with missing values in either gene expression or metadata are omitted by the underlying call to lm/lmer.

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) 

# Step 1: fit linear mixed model on gene expression
# If categorical 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 ) )

# Note: fitExtractVarPartModel also accepts ExpressionSet
data(sample.ExpressionSet, package="Biobase")

# ExpressionSet example
form <- ~ (1|sex) + (1|type) + score
info2 <- pData(sample.ExpressionSet)
varPart2 <- fitExtractVarPartModel( sample.ExpressionSet, form, info2 )

# stop cluster
stopCluster(cl)