varPartConfInf {variancePartition} | R Documentation

## Linear mixed model confidence intervals

### Description

Fit linear mixed model to estimate contribution of multiple sources of variation while simultaneously correcting for all other variables. Then perform parametric bootstrap sampling to get a 95% confidence intervals for each variable for each gene.

### Usage

    varPartConfInf(exprObj, formula, data, REML = FALSE, useWeights = TRUE,
      weightsMatrix = NULL, adjust = NULL, adjustAll = FALSE,
      showWarnings = TRUE, colinearityCutoff = 0.999,
      control = lme4::lmerControl(calc.derivs = FALSE, check.rankX =
      "stop.deficient"), nsim = 1000, ...)

### 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)
`colinearityCutoff` | cutoff used to determine if model is computationally singular
`control` | control settings for lmer()
`nsim` | number of bootstrap datasets
`...` | Additional arguments for lmer() or lm()

### Details

A linear mixed model is fit for each gene, and bootMer() is used to generate parametric bootstrap confidence intervals. use.u=TRUE is used so that the \hat(u) values from the random effects are used as estimated and are not re-sampled. This gives confidence intervals as if additional data were generated from these same current samples. Conversely, use.u=FALSE assumes that this dataset is a sample from a larger population. Thus it simulates \hat(u) based on the estimated variance parameter. This approach gives confidence intervals as if additional data were collected from the larger population from which this dataset is sampled. Overall, use.u=TRUE gives smaller confidence intervals that are appropriate in this case.

### Value

list() of where each entry is the result for a gene. Each entry is a matrix of the 95% confidence interval of the variance fraction for each variable

### 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)

    # Compute bootstrap confidence intervals for each variable for each gene
    resCI <- varPartConfInf( geneExpr[1:5,], form, info, nsim=100 )

    # stop cluster
    stopCluster(cl)

[Package variancePartition version 1.12.3 Index]