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 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## 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: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] a4Reporting_1.52.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.35     R6_2.5.1          fastmap_1.1.1     xfun_0.43        
##  [5] cachem_1.0.8      knitr_1.46        htmltools_0.5.8.1 rmarkdown_2.26   
##  [9] lifecycle_1.0.4   cli_3.6.2         xtable_1.8-4      sass_0.4.9       
## [13] jquerylib_0.1.4   compiler_4.4.0    tools_4.4.0       evaluate_0.23    
## [17] bslib_0.7.0       yaml_2.3.8        rlang_1.1.3       jsonlite_1.8.8