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 4.2.0 RC (2022-04-21 r82226)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## 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       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] a4Reporting_1.45.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.29   R6_2.5.1        xtable_1.8-4    jsonlite_1.8.0 
##  [5] magrittr_2.0.3  evaluate_0.15   stringi_1.7.6   rlang_1.0.2    
##  [9] cli_3.3.0       jquerylib_0.1.4 bslib_0.3.1     rmarkdown_2.14 
## [13] tools_4.2.0     stringr_1.4.0   xfun_0.30       yaml_2.3.5     
## [17] fastmap_1.1.0   compiler_4.2.0  htmltools_0.5.2 knitr_1.38     
## [21] sass_0.4.1