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 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## 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
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## 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_3.20.0 AnnotationDbi_1.68.0
## [4] IRanges_2.40.0 S4Vectors_0.44.0 ALL_1.47.0
## [7] Biobase_2.66.0 BiocGenerics_0.52.0 a4Preproc_1.54.0
##
## loaded via a namespace (and not attached):
## [1] bit_4.5.0 jsonlite_1.8.9 compiler_4.4.1
## [4] crayon_1.5.3 blob_1.2.4 Biostrings_2.74.0
## [7] jquerylib_0.1.4 png_0.1-8 yaml_2.3.10
## [10] fastmap_1.2.0 R6_2.5.1 XVector_0.46.0
## [13] GenomeInfoDb_1.42.0 knitr_1.48 GenomeInfoDbData_1.2.13
## [16] DBI_1.2.3 bslib_0.8.0 rlang_1.1.4
## [19] KEGGREST_1.46.0 cachem_1.1.0 xfun_0.48
## [22] sass_0.4.9 bit64_4.5.2 RSQLite_2.3.7
## [25] memoise_2.0.1 cli_3.6.3 zlibbioc_1.52.0
## [28] digest_0.6.37 lifecycle_1.0.4 vctrs_0.6.5
## [31] evaluate_1.0.1 rmarkdown_2.28 httr_1.4.7
## [34] pkgconfig_2.0.3 tools_4.4.1 htmltools_0.5.8.1
## [37] UCSC.utils_1.2.0