This document explains the functionalities available in the a4Core package.
This package contains utility functions for the Automated Affymetrix Array Analysis suite of packages.
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:
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’.
## R version 4.4.0 RC (2024-04-16 r86468)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.20-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_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
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] a4Core_1.53.0
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.2 knitr_1.46 rlang_1.1.3
## [4] xfun_0.43 jsonlite_1.8.8 htmltools_0.5.8.1
## [7] sass_0.4.9 glmnet_4.1-8 Biobase_2.65.0
## [10] rmarkdown_2.26 grid_4.4.0 evaluate_0.23
## [13] jquerylib_0.1.4 fastmap_1.1.1 yaml_2.3.8
## [16] foreach_1.5.2 lifecycle_1.0.4 compiler_4.4.0
## [19] codetools_0.2-20 Rcpp_1.0.12 lattice_0.22-6
## [22] digest_0.6.35 R6_2.5.1 splines_4.4.0
## [25] shape_1.4.6.1 bslib_0.7.0 Matrix_1.7-0
## [28] tools_4.4.0 iterators_1.0.14 BiocGenerics_0.51.0
## [31] survival_3.6-4 cachem_1.0.8