# Vignette of the a4Reporting package

# 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.

# Create an annotation table

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

# 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.

# Appendix

## Session information

    ## R version 4.6.0 (2026-04-24)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
    ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
    ##  [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: Etc/UTC
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] a4Reporting_1.60.0 rmarkdown_2.31
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] digest_0.6.39    R6_2.6.1         fastmap_1.2.0    xfun_0.57
    ##  [5] maketools_1.3.2  cachem_1.1.0     knitr_1.51       htmltools_0.5.9
    ##  [9] buildtools_1.0.0 lifecycle_1.0.5  cli_3.6.6        xtable_1.8-8
    ## [13] sass_0.4.10      jquerylib_0.1.4  compiler_4.6.0   sys_3.4.3
    ## [17] tools_4.6.0      evaluate_1.0.5   bslib_0.10.0     yaml_2.3.12
    ## [21] jsonlite_2.0.0   rlang_1.2.0