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 1print(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 4.2.1 (2022-06-23)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.0
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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 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_1.60.0
## [4] IRanges_2.32.0 S4Vectors_0.36.0 ALL_1.39.0
## [7] Biobase_2.58.0 BiocGenerics_0.44.0 a4Preproc_1.46.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.9 GenomeInfoDb_1.34.2 XVector_0.38.0
## [4] bslib_0.3.1 compiler_4.2.1 jquerylib_0.1.4
## [7] bitops_1.0-7 zlibbioc_1.44.0 tools_4.2.1
## [10] digest_0.6.29 bit_4.0.4 jsonlite_1.8.0
## [13] evaluate_0.15 RSQLite_2.2.14 memoise_2.0.1
## [16] pkgconfig_2.0.3 png_0.1-7 rlang_1.0.4
## [19] DBI_1.1.3 cli_3.3.0 yaml_2.3.5
## [22] xfun_0.31 fastmap_1.1.0 GenomeInfoDbData_1.2.8
## [25] stringr_1.4.0 httr_1.4.3 knitr_1.39
## [28] Biostrings_2.66.0 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_1.38.0 stringi_1.7.8 RCurl_1.98-1.7
## [40] cachem_1.0.6 crayon_1.5.1