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 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [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_3.19.1 AnnotationDbi_1.66.0
## [4] IRanges_2.38.0 S4Vectors_0.42.0 ALL_1.45.0
## [7] Biobase_2.64.0 BiocGenerics_0.50.0 a4Preproc_1.52.0
##
## loaded via a namespace (and not attached):
## [1] bit_4.0.5 jsonlite_1.8.8 compiler_4.4.0
## [4] crayon_1.5.2 blob_1.2.4 Biostrings_2.72.0
## [7] jquerylib_0.1.4 png_0.1-8 yaml_2.3.8
## [10] fastmap_1.1.1 R6_2.5.1 XVector_0.44.0
## [13] GenomeInfoDb_1.40.0 knitr_1.46 GenomeInfoDbData_1.2.12
## [16] DBI_1.2.2 bslib_0.7.0 rlang_1.1.3
## [19] KEGGREST_1.44.0 cachem_1.0.8 xfun_0.43
## [22] sass_0.4.9 bit64_4.0.5 RSQLite_2.3.6
## [25] memoise_2.0.1 cli_3.6.2 zlibbioc_1.50.0
## [28] digest_0.6.35 lifecycle_1.0.4 vctrs_0.6.5
## [31] evaluate_0.23 rmarkdown_2.26 httr_1.4.7
## [34] pkgconfig_2.0.3 tools_4.4.0 htmltools_0.5.8.1
## [37] UCSC.utils_1.0.0