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 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-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 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] hgu95av2.db_3.2.3 org.Hs.eg.db_3.13.0 AnnotationDbi_1.54.0
## [4] IRanges_2.26.0 S4Vectors_0.30.0 ALL_1.33.0
## [7] Biobase_2.52.0 BiocGenerics_0.38.0 a4Preproc_1.40.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.6 XVector_0.32.0 GenomeInfoDb_1.28.0
## [4] bslib_0.2.5.1 compiler_4.1.0 jquerylib_0.1.4
## [7] zlibbioc_1.38.0 bitops_1.0-7 tools_4.1.0
## [10] digest_0.6.27 bit_4.0.4 jsonlite_1.7.2
## [13] evaluate_0.14 RSQLite_2.2.7 memoise_2.0.0
## [16] pkgconfig_2.0.3 png_0.1-7 rlang_0.4.11
## [19] DBI_1.1.1 yaml_2.2.1 xfun_0.23
## [22] fastmap_1.1.0 GenomeInfoDbData_1.2.6 stringr_1.4.0
## [25] httr_1.4.2 knitr_1.33 Biostrings_2.60.0
## [28] sass_0.4.0 vctrs_0.3.8 bit64_4.0.5
## [31] R6_2.5.0 rmarkdown_2.8 blob_1.2.1
## [34] magrittr_2.0.1 htmltools_0.5.1.1 KEGGREST_1.32.0
## [37] stringi_1.6.2 RCurl_1.98-1.3 cachem_1.0.5
## [40] crayon_1.4.1