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 version 4.2.0 RC (2022-04-21 r82226)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## 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       
## 
## 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_3.15.0  AnnotationDbi_1.59.0
## [4] IRanges_2.31.0       S4Vectors_0.35.0     ALL_1.37.0          
## [7] Biobase_2.57.0       BiocGenerics_0.43.0  a4Preproc_1.45.0    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.8.3           XVector_0.37.0         GenomeInfoDb_1.33.0   
##  [4] bslib_0.3.1            compiler_4.2.0         jquerylib_0.1.4       
##  [7] zlibbioc_1.43.0        bitops_1.0-7           tools_4.2.0           
## [10] digest_0.6.29          bit_4.0.4              jsonlite_1.8.0        
## [13] evaluate_0.15          RSQLite_2.2.12         memoise_2.0.1         
## [16] pkgconfig_2.0.3        png_0.1-7              rlang_1.0.2           
## [19] DBI_1.1.2              cli_3.3.0              yaml_2.3.5            
## [22] xfun_0.30              fastmap_1.1.0          GenomeInfoDbData_1.2.8
## [25] stringr_1.4.0          httr_1.4.2             knitr_1.38            
## [28] Biostrings_2.65.0      sass_0.4.1             vctrs_0.4.1           
## [31] bit64_4.0.5            R6_2.5.1               rmarkdown_2.14        
## [34] blob_1.2.3             magrittr_2.0.3         htmltools_0.5.2       
## [37] KEGGREST_1.37.0        stringi_1.7.6          RCurl_1.98-1.6        
## [40] cachem_1.0.6           crayon_1.5.1