1 Introduction

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.

2 Get feature annotation for an ExpressionSet

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 1
print(head(featureData(a4ALL)))
## An object of class 'AnnotatedDataFrame'
##   featureNames: 1000_at 1001_at ... 1005_at (6 total)
##   varLabels: ENTREZID ENSEMBLID SYMBOL GENENAME
##   varMetadata: labelDescription

3 Appendix

3.1 Session information

## R Under development (unstable) (2023-10-22 r85388)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.19-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_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [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_3.18.0  AnnotationDbi_1.65.0
## [4] IRanges_2.37.0       S4Vectors_0.41.0     ALL_1.43.0          
## [7] Biobase_2.63.0       BiocGenerics_0.49.0  a4Preproc_1.51.0    
## 
## loaded via a namespace (and not attached):
##  [1] bit_4.0.5               jsonlite_1.8.7          compiler_4.4.0         
##  [4] crayon_1.5.2            blob_1.2.4              bitops_1.0-7           
##  [7] Biostrings_2.71.0       jquerylib_0.1.4         png_0.1-8              
## [10] yaml_2.3.7              fastmap_1.1.1           R6_2.5.1               
## [13] XVector_0.43.0          GenomeInfoDb_1.39.0     knitr_1.44             
## [16] GenomeInfoDbData_1.2.11 DBI_1.1.3               bslib_0.5.1            
## [19] rlang_1.1.1             KEGGREST_1.43.0         cachem_1.0.8           
## [22] xfun_0.40               sass_0.4.7              bit64_4.0.5            
## [25] RSQLite_2.3.1           memoise_2.0.1           cli_3.6.1              
## [28] zlibbioc_1.49.0         digest_0.6.33           vctrs_0.6.4            
## [31] evaluate_0.22           RCurl_1.98-1.12         rmarkdown_2.25         
## [34] httr_1.4.7              pkgconfig_2.0.3         tools_4.4.0            
## [37] htmltools_0.5.6.1