Contents

1 Getting started

brgedata includes a collection of BRGE omic and exposome data from the same cohort. The diferent objects guarantees a minimum of samples in common between all sets.

Data available in this R package:

Data Type Number of Samples Number of Features Technology Object Name Class
Exposome 110 15 brge_expo ExposomeSet
Transcriptome 75 67528 Affymetrix HTA 2.0 brge_gexp ExpressionSet
Methylome 20 392277 Illumina Human Methylation 450K brge_methy GenomicRatioSet
Proteome 90 47 brge_prot ExpressionSet

sex and age was included as phenotipic data in each set. Moreover, the ExposomeSet includes asthma status and rhinitis status of each sample.

2 Data Resources

2.1 Exposome Data

To load the exposome data, stored in an ExposomeSet, run the follow commands:

data("brge_expo", package = "brgedata")
brge_expo
## Object of class 'ExposomeSet' (storageMode: environment)
##  . exposures description:
##     . categorical:  0 
##     . continuous:  15 
##  . exposures transformation:
##     . categorical: 0 
##     . transformed: 0 
##     . standardized: 0 
##     . imputed: 0 
##  . assayData: 15 exposures 110 individuals
##     . element names: exp, raw 
##     . exposures: Ben_p, ..., PCB153 
##     . individuals: x0001, ..., x0119 
##  . phenoData: 110 individuals 6 phenotypes
##     . individuals: x0001, ..., x0119 
##     . phenotypes: Asthma, ..., Age 
##  . featureData: 15 exposures 12 explanations
##     . exposures: Ben_p, ..., PCB153 
##     . descriptions: Family, ..., .imp 
## experimentData: use 'experimentData(object)'
## Annotation:

The summary of the data contained by brge_expo:

Data Type Number of Samples Number of Features Technology Object Name Class
Exposome 110 15 brge_expo ExposomeSet

2.2 Transcriptome Data

To load the transcriptome data, saved in an ExpressionSet, run the follow commands:

data("brge_gexp", package = "brgedata")
brge_gexp
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 67528 features, 100 samples 
##   element names: exprs 
## protocolData: none
## phenoData
##   sampleNames: x0001 x0002 ... x0139 (100 total)
##   varLabels: age sex
##   varMetadata: labelDescription
## featureData
##   featureNames: TC01000001.hg.1 TC01000002.hg.1 ...
##     TCUn_gl000247000001.hg.1 (67528 total)
##   fvarLabels: transcript_cluster_id probeset_id ... notes (11 total)
##   fvarMetadata: labelDescription
## experimentData: use 'experimentData(object)'
## Annotation:

The summary of the data contained by brge_gexp:

Data Type Number of Samples Number of Features Technology Object Name Class
Transcriptome 75 67528 Affymetrix HTA 2.0 brge_gexp ExpressionSet

2.3 Methylome Data

To load the methylation data, encapsulated in a GenomicRatioSet, run the follow commands:

data("brge_methy", package = "brgedata")
brge_methy
## class: GenomicRatioSet 
## dim: 392277 20 
## metadata(0):
## assays(1): Beta
## rownames(392277): cg13869341 cg24669183 ... cg26251715 cg25640065
## rowData names(14): Forward_Sequence SourceSeq ...
##   Regulatory_Feature_Group DHS
## colnames(20): x0017 x0043 ... x0077 x0079
## colData names(9): age sex ... Mono Neu
## Annotation
##   array: IlluminaHumanMethylation450k
##   annotation: ilmn12.hg19
## Preprocessing
##   Method: NA
##   minfi version: NA
##   Manifest version: NA

The summary of the data contained by brge_methy:

Data Type Number of Samples Number of Features Technology Object Name Class
Methylome 20 392277 Illumina Human Methylation 450K brge_methy GenomicRatioSet

2.4 Proteome Data

To load the protein data, stored in an ExpressionSet, run the follow commands:

data("brge_prot", package = "brgedata")
brge_prot
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 47 features, 90 samples 
##   element names: exprs 
## protocolData: none
## phenoData
##   sampleNames: x0001 x0002 ... x0090 (90 total)
##   varLabels: age sex
##   varMetadata: labelDescription
## featureData
##   featureNames: Adiponectin_ok Alpha1AntitrypsinAAT_ok ...
##     VitaminDBindingProte_ok (47 total)
##   fvarLabels: chr start end
##   fvarMetadata: labelDescription
## experimentData: use 'experimentData(object)'
## Annotation:

The summary of the data contained by brge_prot:

Data Type Number of Samples Number of Features Technology Object Name Class
Proteome 90 47 brge_prot ExpressionSet

Session info

## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-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] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] minfi_1.44.0                bumphunter_1.40.0          
##  [3] locfit_1.5-9.6              iterators_1.0.14           
##  [5] foreach_1.5.2               Biostrings_2.66.0          
##  [7] XVector_0.38.0              SummarizedExperiment_1.28.0
##  [9] MatrixGenerics_1.10.0       matrixStats_0.62.0         
## [11] GenomicRanges_1.50.0        GenomeInfoDb_1.34.0        
## [13] IRanges_2.32.0              S4Vectors_0.36.0           
## [15] rexposome_1.20.0            Biobase_2.58.0             
## [17] BiocGenerics_0.44.0         BiocStyle_2.26.0           
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.2                gmm_1.7                  
##   [3] tidyselect_1.2.0          lme4_1.1-31              
##   [5] RSQLite_2.2.18            AnnotationDbi_1.60.0     
##   [7] htmlwidgets_1.5.4         FactoMineR_2.6           
##   [9] grid_4.2.1                BiocParallel_1.32.0      
##  [11] norm_1.0-10.0             munsell_0.5.0            
##  [13] preprocessCore_1.60.0     codetools_0.2-18         
##  [15] interp_1.1-3              DT_0.26                  
##  [17] colorspace_2.0-3          filelock_1.0.2           
##  [19] knitr_1.40                rstudioapi_0.14          
##  [21] leaps_3.1                 emmeans_1.8.2            
##  [23] GenomeInfoDbData_1.2.9    bit64_4.0.5              
##  [25] rhdf5_2.42.0              coda_0.19-4              
##  [27] vctrs_0.5.0               generics_0.1.3           
##  [29] TH.data_1.1-1             xfun_0.34                
##  [31] BiocFileCache_2.6.0       R6_2.5.1                 
##  [33] illuminaio_0.40.0         bitops_1.0-7             
##  [35] rhdf5filters_1.10.0       cachem_1.0.6             
##  [37] reshape_0.8.9             DelayedArray_0.24.0      
##  [39] assertthat_0.2.1          BiocIO_1.8.0             
##  [41] scales_1.2.1              multcomp_1.4-20          
##  [43] nnet_7.3-18               gtable_0.3.1             
##  [45] multcompView_0.1-8        lsr_0.5.2                
##  [47] sandwich_3.0-2            rlang_1.0.6              
##  [49] genefilter_1.80.0         scatterplot3d_0.3-42     
##  [51] GlobalOptions_0.1.2       splines_4.2.1            
##  [53] rtracklayer_1.58.0        GEOquery_2.66.0          
##  [55] impute_1.72.0             checkmate_2.1.0          
##  [57] BiocManager_1.30.19       yaml_2.3.6               
##  [59] reshape2_1.4.4            GenomicFeatures_1.50.1   
##  [61] backports_1.4.1           Hmisc_4.7-1              
##  [63] tools_4.2.1               bookdown_0.29            
##  [65] nor1mix_1.3-0             ggplot2_3.3.6            
##  [67] ellipsis_0.3.2            gplots_3.1.3             
##  [69] jquerylib_0.1.4           RColorBrewer_1.1-3       
##  [71] siggenes_1.72.0           Rcpp_1.0.9               
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##  [87] magrittr_2.0.3            data.table_1.14.4        
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##  [97] mclust_6.0.0              gridExtra_2.3            
##  [99] shape_1.4.6               compiler_4.2.1           
## [101] biomaRt_2.54.0            tibble_3.1.8             
## [103] KernSmooth_2.23-20        crayon_1.5.2             
## [105] minqa_1.2.5               htmltools_0.5.3          
## [107] tzdb_0.3.0                Formula_1.2-4            
## [109] tidyr_1.2.1               DBI_1.1.3                
## [111] corrplot_0.92             dbplyr_2.2.1             
## [113] MASS_7.3-58.1             tmvtnorm_1.5             
## [115] rappdirs_0.3.3            boot_1.3-28              
## [117] readr_2.1.3               Matrix_1.5-1             
## [119] cli_3.4.1                 imputeLCMD_2.1           
## [121] pryr_0.1.5                quadprog_1.5-8           
## [123] pkgconfig_2.0.3           flashClust_1.01-2        
## [125] GenomicAlignments_1.34.0  foreign_0.8-83           
## [127] xml2_1.3.3                annotate_1.76.0          
## [129] bslib_0.4.0               rngtools_1.5.2           
## [131] multtest_2.54.0           beanplot_1.3.1           
## [133] estimability_1.4.1        scrime_1.3.5             
## [135] doRNG_1.8.2               stringr_1.4.1            
## [137] digest_0.6.30             base64_2.0.1             
## [139] rmarkdown_2.17            htmlTable_2.4.1          
## [141] DelayedMatrixStats_1.20.0 restfulr_0.0.15          
## [143] curl_4.3.3                Rsamtools_2.14.0         
## [145] gtools_3.9.3              rjson_0.2.21             
## [147] nloptr_2.0.3              lifecycle_1.0.3          
## [149] nlme_3.1-160              jsonlite_1.8.3           
## [151] Rhdf5lib_1.20.0           askpass_1.1              
## [153] limma_3.54.0              fansi_1.0.3              
## [155] pillar_1.8.1              lattice_0.20-45          
## [157] KEGGREST_1.38.0           fastmap_1.1.0            
## [159] httr_1.4.4                survival_3.4-0           
## [161] glue_1.6.2                png_0.1-7                
## [163] glmnet_4.1-4              bit_4.0.4                
## [165] stringi_1.7.8             sass_0.4.2               
## [167] HDF5Array_1.26.0          blob_1.2.3               
## [169] latticeExtra_0.6-30       caTools_1.18.2           
## [171] memoise_2.0.1             dplyr_1.0.10