This document explains the functionalities available in the a4Preproc package.
This package contains utility functions to pre-process data for the Automated Affymetrix Array Analysis suite of packages.
The feature annotation for a specific dataset, as required by the pipeline is extracted with the addGeneInfo function.
library(ALL)
data(ALL)
a4ALL <- addGeneInfo(eset = ALL)
print(head(fData(a4ALL)))## ENTREZID ENSEMBLID SYMBOL
## 1000_at 5595 ENSG00000102882 MAPK3
## 1001_at 7075 ENSG00000066056 TIE1
## 1002_f_at 1557 ENSG00000165841 CYP2C19
## 1003_s_at 643 ENSG00000160683 CXCR5
## 1004_at 643 ENSG00000160683 CXCR5
## 1005_at 1843 ENSG00000120129 DUSP1
## GENENAME
## 1000_at mitogen-activated protein kinase 3
## 1001_at tyrosine kinase with immunoglobulin like and EGF like domains 1
## 1002_f_at cytochrome P450 family 2 subfamily C member 19
## 1003_s_at C-X-C motif chemokine receptor 5
## 1004_at C-X-C motif chemokine receptor 5
## 1005_at dual specificity phosphatase 1print(head(featureData(a4ALL)))## An object of class 'AnnotatedDataFrame'
## featureNames: 1000_at 1001_at ... 1005_at (6 total)
## varLabels: ENTREZID ENSEMBLID SYMBOL GENENAME
## varMetadata: labelDescription## R version 4.6.0 RC (2026-04-17 r89917)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
##
## 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] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] hgu95av2.db_3.13.0 org.Hs.eg.db_3.23.1 AnnotationDbi_1.73.1
## [4] IRanges_2.45.0 S4Vectors_0.49.2 ALL_1.53.0
## [7] Biobase_2.71.0 BiocGenerics_0.57.1 generics_0.1.4
## [10] a4Preproc_1.59.0
##
## loaded via a namespace (and not attached):
## [1] bit_4.6.0 jsonlite_2.0.0 compiler_4.6.0 crayon_1.5.3
## [5] blob_1.3.0 Biostrings_2.79.5 jquerylib_0.1.4 Seqinfo_1.1.0
## [9] png_0.1-9 yaml_2.3.12 fastmap_1.2.0 R6_2.6.1
## [13] XVector_0.51.0 knitr_1.51 DBI_1.3.0 bslib_0.10.0
## [17] rlang_1.2.0 KEGGREST_1.51.1 cachem_1.1.0 xfun_0.57
## [21] sass_0.4.10 bit64_4.6.0-1 otel_0.2.0 RSQLite_2.4.6
## [25] memoise_2.0.1 cli_3.6.6 digest_0.6.39 lifecycle_1.0.5
## [29] vctrs_0.7.3 evaluate_1.0.5 rmarkdown_2.31 httr_1.4.8
## [33] tools_4.6.0 pkgconfig_2.0.3 htmltools_0.5.9