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 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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=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: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] a4Reporting_1.53.0 rmarkdown_2.28    
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37     R6_2.5.1          fastmap_1.2.0     xfun_0.47        
##  [5] maketools_1.3.0   cachem_1.1.0      knitr_1.48        htmltools_0.5.8.1
##  [9] buildtools_1.0.0  lifecycle_1.0.4   cli_3.6.3         xtable_1.8-4     
## [13] sass_0.4.9        jquerylib_0.1.4   compiler_4.4.1    sys_3.4.2        
## [17] tools_4.4.1       evaluate_1.0.0    bslib_0.8.0       yaml_2.3.10      
## [21] jsonlite_1.8.9    rlang_1.1.4