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 4.5.0 beta (2025-04-02 r88102)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.22-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_3.21.0 AnnotationDbi_1.71.0
## [4] IRanges_2.43.0 S4Vectors_0.47.0 ALL_1.49.0
## [7] Biobase_2.69.0 BiocGenerics_0.55.0 generics_0.1.3
## [10] a4Preproc_1.57.0
##
## loaded via a namespace (and not attached):
## [1] bit_4.6.0 jsonlite_2.0.0 compiler_4.5.0
## [4] crayon_1.5.3 blob_1.2.4 Biostrings_2.77.0
## [7] jquerylib_0.1.4 png_0.1-8 yaml_2.3.10
## [10] fastmap_1.2.0 R6_2.6.1 XVector_0.49.0
## [13] GenomeInfoDb_1.45.0 knitr_1.50 GenomeInfoDbData_1.2.14
## [16] DBI_1.2.3 bslib_0.9.0 rlang_1.1.6
## [19] KEGGREST_1.49.0 cachem_1.1.0 xfun_0.52
## [22] sass_0.4.10 bit64_4.6.0-1 RSQLite_2.3.9
## [25] memoise_2.0.1 cli_3.6.4 digest_0.6.37
## [28] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.3
## [31] rmarkdown_2.29 httr_1.4.7 pkgconfig_2.0.3
## [34] tools_4.5.0 htmltools_0.5.8.1 UCSC.utils_1.5.0