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 4.1.0 RC (2021-05-16 r80304)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Mojave 10.14.6
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
## [1] hgu95av2.db_3.2.3    org.Hs.eg.db_3.13.0  AnnotationDbi_1.55.0
## [4] IRanges_2.27.0       S4Vectors_0.31.0     ALL_1.33.0          
## [7] Biobase_2.53.0       BiocGenerics_0.39.0  a4Preproc_1.41.0    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.6             XVector_0.33.0         GenomeInfoDb_1.29.0   
##  [4] bslib_0.2.5.1          compiler_4.1.0         jquerylib_0.1.4       
##  [7] zlibbioc_1.39.0        bitops_1.0-7           tools_4.1.0           
## [10] digest_0.6.27          bit_4.0.4              jsonlite_1.7.2        
## [13] evaluate_0.14          RSQLite_2.2.7          memoise_2.0.0         
## [16] pkgconfig_2.0.3        png_0.1-7              rlang_0.4.11          
## [19] DBI_1.1.1              yaml_2.2.1             xfun_0.23             
## [22] fastmap_1.1.0          GenomeInfoDbData_1.2.6 stringr_1.4.0         
## [25] httr_1.4.2             knitr_1.33             Biostrings_2.61.0     
## [28] sass_0.4.0             vctrs_0.3.8            bit64_4.0.5           
## [31] R6_2.5.0               rmarkdown_2.8          blob_1.2.1            
## [34] magrittr_2.0.1         htmltools_0.5.1.1      KEGGREST_1.33.0       
## [37] stringi_1.6.2          RCurl_1.98-1.3         cachem_1.0.5          
## [40] crayon_1.4.1