Date: 2025-10-29

# Vignette of the a4Reporting package

#### 2025-10-29

# 1 Introduction

This document explains the functionalities available in the a4Reporting package.

This package contains utility functions to enhance reporting of data for the Automated Affymetrix Array Analysis suite of packages.

# 2 Create an annotation table

The `annotationTable` function enhances the reporting of table of genes or gene ontology term.

# 3 Top table of classification objects

A few utility functions to enhances the reporting of top tables for `glmnet`, `lognet`, `elnet`, `pam` and `pam` classification confusion are available.

# 4 Appendix

## 4.1 Session information

    ## R version 4.5.1 Patched (2025-08-23 r88802)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.3 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.22-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] a4Reporting_1.58.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] digest_0.6.37     R6_2.6.1          fastmap_1.2.0     xfun_0.53
    ##  [5] cachem_1.1.0      knitr_1.50        htmltools_0.5.8.1 rmarkdown_2.30
    ##  [9] lifecycle_1.0.4   cli_3.6.5         xtable_1.8-4      sass_0.4.10
    ## [13] jquerylib_0.1.4   compiler_4.5.1    tools_4.5.1       evaluate_1.0.5
    ## [17] bslib_0.9.0       yaml_2.3.10       rlang_1.1.6       jsonlite_2.0.0