Date: 2026-04-28

# Vignette of the a4Core package

#### 2026-04-28

# 1 Introduction

This document explains the functionalities available in the a4Core package.

This package contains utility functions for the Automated Affymetrix Array Analysis suite of packages.

# 2 Simulate data

An expressionSet example data for testing and demonstration of the set of packages is simulated with the `simulateData` function:

    eSet <- simulateData(
        nCols = 40, nRows = 1000,
        nEffectRows = 5, nNoEffectCols = 5,
        betweenClassDifference = 1, withinClassSd = 0.5
    )
    print(eSet)

    ## ExpressionSet (storageMode: lockedEnvironment)
    ## assayData: 1000 features, 40 samples
    ##   element names: exprs
    ## protocolData: none
    ## phenoData
    ##   sampleNames: Sample1 Sample2 ... Sample40 (40 total)
    ##   varLabels: type
    ##   varMetadata: type labelDescription
    ## featureData: none
    ## experimentData: use 'experimentData(object)'
    ## Annotation:

# 3 Top tables utility functions for classification

The package contains utility functions to create the top tables of the most important features for multiple classification models as produced by the `lassoClass` function of the `a4Classif` package, as ‘glmnet’, ‘lognet’ and ‘elnet’.

# 4 Appendix

## 4.1 Session information

    ## R version 4.6.0 RC (2026-04-17 r89917)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so
    ## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_GB              LC_COLLATE=C
    ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
    ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    ##
    ## time zone: America/New_York
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] a4Core_1.60.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] cli_3.6.6           knitr_1.51          rlang_1.2.0
    ##  [4] xfun_0.57           otel_0.2.0          generics_0.1.4
    ##  [7] jsonlite_2.0.0      htmltools_0.5.9     sass_0.4.10
    ## [10] glmnet_4.1-10       Biobase_2.72.0      rmarkdown_2.31
    ## [13] grid_4.6.0          evaluate_1.0.5      jquerylib_0.1.4
    ## [16] fastmap_1.2.0       yaml_2.3.12         foreach_1.5.2
    ## [19] lifecycle_1.0.5     compiler_4.6.0      codetools_0.2-20
    ## [22] Rcpp_1.1.1-1.1      lattice_0.22-9      digest_0.6.39
    ## [25] R6_2.6.1            splines_4.6.0       shape_1.4.6.1
    ## [28] bslib_0.10.0        Matrix_1.7-5        tools_4.6.0
    ## [31] iterators_1.0.14    BiocGenerics_0.58.0 survival_3.8-6
    ## [34] cachem_1.1.0