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 Under development (unstable) (2021-01-19 r79848)
## 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_US.UTF-8        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] minfi_1.37.0                bumphunter_1.33.0          
##  [3] locfit_1.5-9.4              iterators_1.0.13           
##  [5] foreach_1.5.1               Biostrings_2.59.2          
##  [7] XVector_0.31.1              SummarizedExperiment_1.21.1
##  [9] MatrixGenerics_1.3.1        matrixStats_0.58.0         
## [11] GenomicRanges_1.43.3        GenomeInfoDb_1.27.5        
## [13] IRanges_2.25.6              S4Vectors_0.29.7           
## [15] rexposome_1.13.2            Biobase_2.51.0             
## [17] BiocGenerics_0.37.1         BiocStyle_2.19.1           
## 
## loaded via a namespace (and not attached):
##   [1] gmm_1.6-5                 tidyselect_1.1.0         
##   [3] lme4_1.1-26               RSQLite_2.2.3            
##   [5] AnnotationDbi_1.53.0      htmlwidgets_1.5.3        
##   [7] FactoMineR_2.4            grid_4.1.0               
##   [9] BiocParallel_1.25.3       norm_1.0-9.5             
##  [11] munsell_0.5.0             codetools_0.2-18         
##  [13] preprocessCore_1.53.1     statmod_1.4.35           
##  [15] DT_0.17                   colorspace_2.0-0         
##  [17] filelock_1.0.2            knitr_1.31               
##  [19] rstudioapi_0.13           leaps_3.1                
##  [21] GenomeInfoDbData_1.2.4    bit64_4.0.5              
##  [23] rhdf5_2.35.0              vctrs_0.3.6              
##  [25] generics_0.1.0            xfun_0.20                
##  [27] BiocFileCache_1.15.1      R6_2.5.0                 
##  [29] illuminaio_0.33.0         bitops_1.0-6             
##  [31] rhdf5filters_1.3.3        cachem_1.0.2             
##  [33] reshape_0.8.8             DelayedArray_0.17.7      
##  [35] assertthat_0.2.1          BiocIO_1.1.2             
##  [37] scales_1.1.1              nnet_7.3-15              
##  [39] gtable_0.3.0              lsr_0.5                  
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##  [43] genefilter_1.73.1         scatterplot3d_0.3-41     
##  [45] GlobalOptions_0.1.2       splines_4.1.0            
##  [47] rtracklayer_1.51.4        GEOquery_2.59.0          
##  [49] impute_1.65.0             checkmate_2.0.0          
##  [51] BiocManager_1.30.10       yaml_2.2.1               
##  [53] reshape2_1.4.4            GenomicFeatures_1.43.3   
##  [55] backports_1.2.1           Hmisc_4.4-2              
##  [57] tools_4.1.0               bookdown_0.21            
##  [59] nor1mix_1.3-0             ggplot2_3.3.3            
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##  [67] base64enc_0.1-3           sparseMatrixStats_1.3.6  
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##  [89] mclust_5.4.7              gridExtra_2.3            
##  [91] shape_1.4.5               compiler_4.1.0           
##  [93] biomaRt_2.47.4            tibble_3.0.6             
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##  [97] minqa_1.2.4               htmltools_0.5.1.1        
##  [99] Formula_1.2-4             tidyr_1.1.2              
## [101] DBI_1.1.1                 corrplot_0.84            
## [103] dbplyr_2.0.0              MASS_7.3-53              
## [105] tmvtnorm_1.4-10           rappdirs_0.3.3           
## [107] boot_1.3-26               readr_1.4.0              
## [109] Matrix_1.3-2              imputeLCMD_2.0           
## [111] pryr_0.1.4                quadprog_1.5-8           
## [113] pkgconfig_2.0.3           flashClust_1.01-2        
## [115] GenomicAlignments_1.27.2  foreign_0.8-81           
## [117] xml2_1.3.2                annotate_1.69.0          
## [119] rngtools_1.5              multtest_2.47.0          
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## [125] digest_0.6.27             rmarkdown_2.6            
## [127] base64_2.0                htmlTable_2.1.0          
## [129] DelayedMatrixStats_1.13.5 restfulr_0.0.13          
## [131] curl_4.3                  Rsamtools_2.7.1          
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## [137] nlme_3.1-151              Rhdf5lib_1.13.0          
## [139] askpass_1.1               limma_3.47.6             
## [141] pillar_1.4.7              lattice_0.20-41          
## [143] fastmap_1.1.0             httr_1.4.2               
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## [147] png_0.1-7                 glmnet_4.1               
## [149] bit_4.0.4                 stringi_1.5.3            
## [151] HDF5Array_1.19.0          blob_1.2.1               
## [153] latticeExtra_0.6-29       caTools_1.18.1           
## [155] memoise_2.0.0             dplyr_1.0.4