1 Introduction

This document explains the functionalities available in the a4Core package.

This package contains utility functions for the Automated Affymetrix Array Analysis suite of packages.

2 Simulate data

An expressionSet example data for testing and demonstration of the set of packages is simulated with the simulateData function:

eSet <- simulateData(
    nCols = 40, nRows = 1000, 
    nEffectRows = 5, nNoEffectCols = 5,
    betweenClassDifference = 1, withinClassSd = 0.5
)
print(eSet)
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 1000 features, 40 samples 
##   element names: exprs 
## protocolData: none
## phenoData
##   sampleNames: Sample1 Sample2 ... Sample40 (40 total)
##   varLabels: type
##   varMetadata: type labelDescription
## featureData: none
## experimentData: use 'experimentData(object)'
## Annotation:

3 Top tables utility functions for classification

The package contains utility functions to create the top tables of the most important features for multiple classification models as produced by the lassoClass function of the a4Classif package, as ‘glmnet’, ‘lognet’ and ‘elnet’.

4 Appendix

4.1 Session information

## R Under development (unstable) (2020-10-17 r79346)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so
## 
## 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       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] a4Core_1.39.0
## 
## loaded via a namespace (and not attached):
##  [1] codetools_0.2-16    lattice_0.20-41     foreach_1.5.1      
##  [4] glmnet_4.0-2        digest_0.6.27       grid_4.1.0         
##  [7] magrittr_1.5        evaluate_0.14       rlang_0.4.8        
## [10] stringi_1.5.3       Matrix_1.2-18       rmarkdown_2.5      
## [13] splines_4.1.0       iterators_1.0.13    tools_4.1.0        
## [16] stringr_1.4.0       Biobase_2.51.0      parallel_4.1.0     
## [19] survival_3.2-7      xfun_0.18           yaml_2.2.1         
## [22] compiler_4.1.0      BiocGenerics_0.37.0 shape_1.4.5        
## [25] htmltools_0.5.0     knitr_1.30