sortCols {variancePartition} | R Documentation

## Sort variance partition statistics

### Description

Sort columns returned by extractVarPart() or fitExtractVarPartModel()

### Usage

    sortCols(x, FUN = median, decreasing = TRUE, last = c("Residuals",
      "Measurement.error"), ...)

    ## S4 method for signature 'matrix'
    sortCols(x, FUN = median, decreasing = TRUE,
      last = c("Residuals", "Measurement.error"), ...)

    ## S4 method for signature 'data.frame'
    sortCols(x, FUN = median, decreasing = TRUE,
      last = c("Residuals", "Measurement.error"), ...)

    ## S4 method for signature 'varPartResults'
    sortCols(x, FUN = median, decreasing = TRUE,
      last = c("Residuals", "Measurement.error"), ...)

### Arguments

`x` | object returned by extractVarPart() or fitExtractVarPartModel()
`FUN` | function giving summary statistic to sort by. Defaults to median
`decreasing` | logical. Should the sorting be increasing or decreasing?
`last` | columns to be placed on the right, regardless of values in these columns
`...` | other arguments to sort

### Value

data.frame with columns sorted by mean value, with Residuals in last column

### Examples

    # 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
    # sort columns by median value
    plotVarPart( sortCols( varPart ) )

    # stop cluster
    stopCluster(cl)

[Package variancePartition version 1.12.3 Index]