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 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
## R version 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.6.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## 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_3.17.0 AnnotationDbi_1.64.0
## [4] IRanges_2.36.0 S4Vectors_0.40.1 ALL_1.43.0
## [7] Biobase_2.62.0 BiocGenerics_0.48.0 a4Preproc_1.50.0
##
## loaded via a namespace (and not attached):
## [1] bit_4.0.5 jsonlite_1.8.7 compiler_4.3.1
## [4] crayon_1.5.2 blob_1.2.4 bitops_1.0-7
## [7] Biostrings_2.70.1 jquerylib_0.1.4 png_0.1-8
## [10] yaml_2.3.7 fastmap_1.1.1 R6_2.5.1
## [13] XVector_0.42.0 GenomeInfoDb_1.38.0 knitr_1.43
## [16] GenomeInfoDbData_1.2.10 DBI_1.1.3 bslib_0.5.0
## [19] rlang_1.1.1 KEGGREST_1.42.0 cachem_1.0.8
## [22] xfun_0.39 sass_0.4.6 bit64_4.0.5
## [25] RSQLite_2.3.1 memoise_2.0.1 cli_3.6.1
## [28] zlibbioc_1.48.0 digest_0.6.33 vctrs_0.6.3
## [31] evaluate_0.21 RCurl_1.98-1.12 rmarkdown_2.23
## [34] httr_1.4.6 pkgconfig_2.0.3 tools_4.3.1
## [37] htmltools_0.5.5