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) (2022-10-25 r83175)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.17-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_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_1.45.0                bumphunter_1.41.0          
##  [3] locfit_1.5-9.6              iterators_1.0.14           
##  [5] foreach_1.5.2               Biostrings_2.67.0          
##  [7] XVector_0.39.0              SummarizedExperiment_1.29.0
##  [9] MatrixGenerics_1.11.0       matrixStats_0.62.0         
## [11] GenomicRanges_1.51.0        GenomeInfoDb_1.35.0        
## [13] IRanges_2.33.0              S4Vectors_0.37.0           
## [15] rexposome_1.21.0            Biobase_2.59.0             
## [17] BiocGenerics_0.45.0         BiocStyle_2.27.0           
## 
## loaded via a namespace (and not attached):
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##   [3] BiocIO_1.9.0              bitops_1.0-7             
##   [5] filelock_1.0.2            tibble_3.1.8             
##   [7] preprocessCore_1.61.0     XML_3.99-0.12            
##   [9] rpart_4.1.19              lifecycle_1.0.3          
##  [11] base64_2.0.1              lattice_0.20-45          
##  [13] MASS_7.3-58.1             scrime_1.3.5             
##  [15] flashClust_1.01-2         backports_1.4.1          
##  [17] magrittr_2.0.3            limma_3.55.0             
##  [19] Hmisc_4.7-1               sass_0.4.2               
##  [21] rmarkdown_2.17            jquerylib_0.1.4          
##  [23] yaml_2.3.6                askpass_1.1              
##  [25] doRNG_1.8.2               DBI_1.1.3                
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## [171] bslib_0.4.0               bit_4.0.4