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) (2021-10-19 r81077)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-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_3.14.0  AnnotationDbi_1.57.0
## [4] IRanges_2.29.0       S4Vectors_0.33.0     ALL_1.35.0          
## [7] Biobase_2.55.0       BiocGenerics_0.41.0  a4Preproc_1.43.0    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7             XVector_0.35.0         GenomeInfoDb_1.31.0   
##  [4] bslib_0.3.1            compiler_4.2.0         jquerylib_0.1.4       
##  [7] zlibbioc_1.41.0        bitops_1.0-7           tools_4.2.0           
## [10] digest_0.6.28          bit_4.0.4              jsonlite_1.7.2        
## [13] RSQLite_2.2.8          evaluate_0.14          memoise_2.0.0         
## [16] pkgconfig_2.0.3        png_0.1-7              rlang_0.4.12          
## [19] DBI_1.1.1              yaml_2.2.1             xfun_0.27             
## [22] fastmap_1.1.0          GenomeInfoDbData_1.2.7 stringr_1.4.0         
## [25] httr_1.4.2             knitr_1.36             Biostrings_2.63.0     
## [28] sass_0.4.0             vctrs_0.3.8            bit64_4.0.5           
## [31] R6_2.5.1               rmarkdown_2.11         blob_1.2.2            
## [34] magrittr_2.0.1         htmltools_0.5.2        KEGGREST_1.35.0       
## [37] stringi_1.7.5          RCurl_1.98-1.5         cachem_1.0.6          
## [40] crayon_1.4.1