This vignette describes the basic usage of the TENET.ExperimentHub package, which contains datasets for use in the TENET package’s vignette and function examples. These include a variety of different objects to illustrate different datasets used in TENET functions. See our GitHub repository (https://github.com/rhielab/TENET.ExperimentHub) for more information. Where applicable, all datasets are aligned to the hg38 human genome.
TENET.ExperimentHub 0.99.3
The TENET.ExperimentHub package contains 6 datasets for use in the TENET
package’s examples and vignettes. These datasets include an example
MultiAssayExperiment object with matched gene expression and DNA methylation
data from a subset of both tumor (case) and adjacent normal (control) samples
in The Cancer Genome Atlas (TCGA)’s breast adenocarcinoma (BRCA) cohort with
essential information used in all TENET functions, an example GRanges object
produced by the TENET step1MakeExternalDatasets function, a
SummarizedExperiment object with example purity data to pass to the TENET
step2GetDifferentiallyMethylatedSites function, a data frame with example
patient clinical data (matching the data in the example MultiAssayExperiment
object), and two additional GRanges objects containing example peak and
topologically associating domain (TAD) data, respectively. Where applicable,
all datasets are aligned to the hg38 human genome.
R 4.5 or a newer version is required.
On Ubuntu 22.04, successful installation required several additional packages. They can be installed by running the following command in a terminal:
sudo apt-get install r-base-dev libcurl4-openssl-dev libfreetype6-dev libfribidi-dev libfontconfig1-dev libharfbuzz-dev libtiff5-dev libxml2-dev
No dependencies other than R are required on macOS or Windows.
Two versions of this package are available.
To install the stable version from Bioconductor, start R and run:
## Install BiocManager, which is required to install packages from Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install(version = "devel")
BiocManager::install("TENET.ExperimentHub")The development version containing the most recent updates is available from our GitHub repository (https://github.com/rhielab/TENET.ExperimentHub).
To install the development version from GitHub, start R and run:
## Install prerequisite packages to install the development version from GitHub
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
BiocManager::install(version = "devel")
BiocManager::install("rhielab/TENET.ExperimentHub")To load the TENET.ExperimentHub package, start R and run:
library(TENET.ExperimentHub)Wrapper functions are provided to allow easy access to all included datasets. Usage of each wrapper function is demonstrated below.
exampleTENETMultiAssayExperimentA MultiAssayExperiment dataset created using a modified version
of the TCGADownloader function from the TENET package utilizing
TCGAbiolinks package functionality. This object contains two
SummarizedExperiment objects, expression and methylation, with
expression data for 11,637 genes annotated to the GENCODE v36 dataset,
including all 1,637 identified human TF genes, and DNA methylation data for
20,000 probes from the Illumina HM450 methylation array. The data are
aligned to the human hg38 genome. Expression and methylation values were
matched from 200 tumor and 42 adjacent normal tissue samples subset from the
TCGA BRCA dataset. Additionally, results from running the TENET step 1-6
functions on these samples are included in the metadata of this
MultiAssayExperiment object. Clinical data for these samples are included in
the colData of the MultiAssayExperiment object. (A separate data frame
object containing a subset of the clinical data for these samples is
available as exampleTENETClinicalDataFrame.) This dataset is included to
demonstrate TENET functions. Note: Because this dataset is a small subset of
the overall BRCA dataset, results generated by TENET from this dataset
differ from those presented for the BRCA dataset at large in TENET
publications.
## Retrieve the ExperimentHub metadata for the object
exampleTENETMultiAssayExperiment(metadata = TRUE)
#> ExperimentHub with 1 record
#> # snapshotDate(): 2025-03-17
#> # names(): EH9587
#> # package(): TENET.ExperimentHub
#> # $dataprovider: TCGA
#> # $species: Homo sapiens
#> # $rdataclass: MultiAssayExperiment
#> # $rdatadateadded: 2024-09-13
#> # $title: exampleTENETMultiAssayExperiment
#> # $description: A MultiAssayExperiment dataset created using a modified vers...
#> # $taxonomyid: 9606
#> # $genome: hg38
#> # $sourcetype: Multiple
#> # $sourceurl: https://bioconductor.org/packages/release/bioc/html/TCGAbiolin...
#> # $sourcesize: NA
#> # $tags: c("CancerData", "clinical", "CopyNumberVariationData",
#> # "DNAMethylationData", "ExpressionData", "Homo_sapiens_Data",
#> # "Survival", "TCGA", "TENET")
#> # retrieve record with 'object[["EH9587"]]'
## Retrieve the object itself
exampleTENETMultiAssayExperiment()
#> see ?TENET.ExperimentHub and browseVignettes('TENET.ExperimentHub') for documentation
#> loading from cache
#> require("MultiAssayExperiment")
#> A MultiAssayExperiment object of 2 listed
#> experiments with user-defined names and respective classes.
#> Containing an ExperimentList class object of length 2:
#> [1] expression: RangedSummarizedExperiment with 11637 rows and 242 columns
#> [2] methylation: RangedSummarizedExperiment with 20000 rows and 242 columns
#> Functionality:
#> experiments() - obtain the ExperimentList instance
#> colData() - the primary/phenotype DataFrame
#> sampleMap() - the sample coordination DataFrame
#> `$`, `[`, `[[` - extract colData columns, subset, or experiment
#> *Format() - convert into a long or wide DataFrame
#> assays() - convert ExperimentList to a SimpleList of matrices
#> exportClass() - save data to flat filesexampleTENETClinicalDataFrameA data frame containing example and simulated clinical
information corresponding to the samples in the
exampleTENETMultiAssayExperiment object, used to demonstrate how TENET
functions can import clinical data from a specified data frame. Clinical
data are utilized by the step2GetDifferentiallyMethylatedSites,
step7TopGenesSurvival, and step7ExpressionVsDNAMethylationScatterplots
functions. The data frame consists of vital status and time variables for
use by the step7TopGenesSurvival function, simulated purity data for each
sample, and simulated copy number variation (CNV) and somatic mutation (SM)
data for the top 10 genes by number of linked hypermethylated and
hypomethylated probes derived from analyses done using the
exampleTENETMultiAssayExperiment object. These data are a subset of the
clinical data contained in the colData of the
exampleTENETMultiAssayExperiment object.
## Retrieve the ExperimentHub metadata for the object
exampleTENETClinicalDataFrame(metadata = TRUE)
#> ExperimentHub with 1 record
#> # snapshotDate(): 2025-03-17
#> # names(): EH9588
#> # package(): TENET.ExperimentHub
#> # $dataprovider: Multiple
#> # $species: Homo sapiens
#> # $rdataclass: data.frame
#> # $rdatadateadded: 2024-09-13
#> # $title: exampleTENETClinicalDataFrame
#> # $description: A data frame containing example and simulated clinical infor...
#> # $taxonomyid: 9606
#> # $genome: NA
#> # $sourcetype: Multiple
#> # $sourceurl: https://bioconductor.org/packages/release/bioc/html/TCGAbiolin...
#> # $sourcesize: NA
#> # $tags: c("CancerData", "clinical", "CopyNumberVariationData",
#> # "ExpressionData", "Homo_sapiens_Data", "Survival", "TCGA", "TENET")
#> # retrieve record with 'object[["EH9588"]]'
## Retrieve the object itself
exampleTENETClinicalDataFrame()
#> see ?TENET.ExperimentHub and browseVignettes('TENET.ExperimentHub') for documentation
#> loading from cache
#> vital_status time purity ENSG00000165821_CNV
#> [ reached 'max' / getOption("max.print") -- omitted 39 columns ]
#> [ reached 'max' / getOption("max.print") -- omitted 231 rows ]exampleTENETStep1MakeExternalDatasetsGRangesA GenomicRanges dataset representing putative enhancer regions
relevant to BRCA, created using the step1MakeExternalDatasets function in
the TENET package with the consensusEnhancer, consensusNDR,
publicEnhancer, publicNDR, and ENCODEdELS arguments all set to TRUE,
and the cancerType argument set to “BRCA”. The data are aligned to the
human hg38 genome. This dataset is included to demonstrate TENET’s
step2GetDifferentiallyMethylatedSites function.
## Retrieve the ExperimentHub metadata for the object
exampleTENETStep1MakeExternalDatasetsGRanges(metadata = TRUE)
#> ExperimentHub with 1 record
#> # snapshotDate(): 2025-03-17
#> # names(): EH9589
#> # package(): TENET.ExperimentHub
#> # $dataprovider: Multiple
#> # $species: Homo sapiens
#> # $rdataclass: GRanges
#> # $rdatadateadded: 2024-09-13
#> # $title: exampleTENETStep1MakeExternalDatasetsGRanges
#> # $description: A GenomicRanges dataset representing putative enhancer regio...
#> # $taxonomyid: 9606
#> # $genome: hg38
#> # $sourcetype: Multiple
#> # $sourceurl: https://github.com/rhielab/TENET.AnnotationHub_files
#> # $sourcesize: NA
#> # $tags: c("CancerData", "ChipSeq", "CopyNumberVariationData",
#> # "DnaseSeq", "ENCODE", "EpigenomeRoadMap", "ExpressionData",
#> # "FANTOM5", "GEO", "H3K27ac", "Homo_sapiens_Data", "peaks", "TCGA",
#> # "TENET")
#> # retrieve record with 'object[["EH9589"]]'
## Retrieve the object itself
exampleTENETStep1MakeExternalDatasetsGRanges()
#> see ?TENET.ExperimentHub and browseVignettes('TENET.ExperimentHub') for documentation
#> loading from cache
#> GRanges object with 1971031 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 10121-10270 *
#> [2] chr1 10389-10400 *
#> [3] chr1 16141-16290 *
#> [4] chr1 20061-20210 *
#> [5] chr1 135126-135275 *
#> ... ... ... ...
#> [1971027] chrM 8917-9607 *
#> [1971028] chrM 9665-9974 *
#> [1971029] chrM 10079-10766 *
#> [1971030] chrM 11143-12241 *
#> [1971031] chrM 12302-16539 *
#> -------
#> seqinfo: 25 sequences from an unspecified genome; no seqlengthsexampleTENETStep2GetDifferentiallyMethylatedSitesPuritySummarizedExperimentSummarizedExperiment object
A SummarizedExperiment object with three DNA methylation
datasets each composed of 10 adjacent normal colorectal adenocarcinoma
(COAD) samples from The Cancer Genome Atlas (TCGA), retrieved using the
TCGAbiolinks package. Each dataset has data for 20,000 probes from the
Illumina HM450 methylation array, to match the number of probes in the
exampleTENETMultiAssayExperiment object. The data are aligned to the human
hg38 genome. This object is representative of a purity dataset, which
would contain DNA methylation data from potentially confounding sources,
used with TENET’s step2GetDifferentiallyMethylatedSites function.
## Retrieve the ExperimentHub metadata for the object
exampleTENETStep2GetDifferentiallyMethylatedSitesPuritySummarizedExperiment(
metadata = TRUE
)
#> ExperimentHub with 1 record
#> # snapshotDate(): 2025-03-17
#> # names(): EH9590
#> # package(): TENET.ExperimentHub
#> # $dataprovider: TCGA
#> # $species: Homo sapiens
#> # $rdataclass: SummarizedExperiment
#> # $rdatadateadded: 2024-09-13
#> # $title: exampleTENETStep2GetDifferentiallyMethylatedSitesPuritySummarizedE...
#> # $description: A SummarizedExperiment object with three DNA methylation dat...
#> # $taxonomyid: 9606
#> # $genome: hg38
#> # $sourcetype: Multiple
#> # $sourceurl: https://bioconductor.org/packages/release/bioc/html/TCGAbiolin...
#> # $sourcesize: NA
#> # $tags: c("CancerData", "CopyNumberVariationData",
#> # "DNAMethylationData", "ExpressionData", "Homo_sapiens_Data", "TCGA",
#> # "TENET")
#> # retrieve record with 'object[["EH9590"]]'
## Retrieve the object itself
exampleTENETStep2GetDifferentiallyMethylatedSitesPuritySummarizedExperiment()
#> see ?TENET.ExperimentHub and browseVignettes('TENET.ExperimentHub') for documentation
#> loading from cache
#> class: RangedSummarizedExperiment
#> dim: 20000 10
#> metadata(0):
#> assays(2): purityMethylationExampleA purityMethylationExampleB
#> rownames(20000): cg00002190 cg00002809 ... rs4331560 rs6982811
#> rowData names(52): address_A address_B ... MASK_extBase MASK_general
#> colnames: NULL
#> colData names(0):exampleTENETPeakRegionsA GenomicRanges dataset with example genomic regions (peaks) of
interest, used to demonstrate TENET’s step7TopGenesUserPeakOverlap
function. The peaks are derived from a ChIP-seq experiment on FOXA1 in MCF-7
cells and aligned to the human hg38 genome. They were downloaded from the
ENCODE portal (file ENCFF112JVK in experiment ENCSR126YEB). Citation: ENCODE
Project Consortium; Moore JE, Purcaro MJ, Pratt HE, et al. Expanded
encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020
Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29.
Erratum in: Nature. 2022 May;605(7909):E3. PMID: 32728249; PMCID: PMC7410828.
## Retrieve the ExperimentHub metadata for the object
exampleTENETPeakRegions(metadata = TRUE)
#> ExperimentHub with 1 record
#> # snapshotDate(): 2025-03-17
#> # names(): EH9591
#> # package(): TENET.ExperimentHub
#> # $dataprovider: ENCODE
#> # $species: Homo sapiens
#> # $rdataclass: GRanges
#> # $rdatadateadded: 2024-09-13
#> # $title: exampleTENETPeakRegions
#> # $description: A GenomicRanges dataset with example genomic regions (peaks)...
#> # $taxonomyid: 9606
#> # $genome: hg38
#> # $sourcetype: BED
#> # $sourceurl: https://www.encodeproject.org/files/ENCFF112JVK/@@download/ENC...
#> # $sourcesize: NA
#> # $tags: c("CancerData", "ChIPSeqData", "CopyNumberVariationData",
#> # "ENCODE", "ExpressionData", "FOXA1", "Homo_sapiens_Data", "peaks",
#> # "TENET")
#> # retrieve record with 'object[["EH9591"]]'
## Retrieve the object itself
exampleTENETPeakRegions()
#> see ?TENET.ExperimentHub and browseVignettes('TENET.ExperimentHub') for documentation
#> loading from cache
#> GRanges object with 37386 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr20 41650340-41650989 *
#> [2] chr1 147612278-147612917 *
#> [3] chr20 48812030-48812609 *
#> [4] chr15 69594337-69595180 *
#> [5] chr8 101607580-101608404 *
#> ... ... ... ...
#> [37382] chr14 101762956-101763345 *
#> [37383] chr16 15875210-15875599 *
#> [37384] chr5 179821648-179822037 *
#> [37385] chr12 84236865-84237254 *
#> [37386] chr17 64985135-64985570 *
#> -------
#> seqinfo: 23 sequences from an unspecified genome; no seqlengthsexampleTENETTADRegionsA GenomicRanges dataset with example topologically associating
domains (TADs), used to demonstrate TENET’s step7TopGenesTADTables
function. The TADs are derived from T47D cells (mistakenly labeled as
‘T470’), and aligned to the human hg38 genome. They were downloaded from the
3D Genome Browser at http://3dgenome.fsm.northwestern.edu. Citation: Wang
Y, Song F, Zhang B, et al. The 3D Genome Browser: a web-based browser for
visualizing 3D genome organization and long-range chromatin interactions.
Genome Biol. 2018 Oct 4;19(1):151. doi: 10.1186/s13059-018-1519-9. PMID:
30286773; PMCID: PMC6172833.
## Retrieve the ExperimentHub metadata for the object
exampleTENETTADRegions(metadata = TRUE)
#> ExperimentHub with 1 record
#> # snapshotDate(): 2025-03-17
#> # names(): EH9592
#> # package(): TENET.ExperimentHub
#> # $dataprovider: 3D Genome Browser
#> # $species: Homo sapiens
#> # $rdataclass: GRanges
#> # $rdatadateadded: 2024-09-13
#> # $title: exampleTENETTADRegions
#> # $description: A GenomicRanges dataset with example topologically associati...
#> # $taxonomyid: 9606
#> # $genome: hg38
#> # $sourcetype: BED
#> # $sourceurl: http://3dgenome.fsm.northwestern.edu/downloads/hg38.TADs.zip
#> # $sourcesize: NA
#> # $tags: c("CancerData", "CopyNumberVariationData", "ExpressionData",
#> # "Homo_sapiens_Data", "TAD", "TENET")
#> # retrieve record with 'object[["EH9592"]]'
## Retrieve the object itself
exampleTENETTADRegions()
#> see ?TENET.ExperimentHub and browseVignettes('TENET.ExperimentHub') for documentation
#> loading from cache
#> GRanges object with 1889 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> 1 chr1 800001-3680000 *
#> 2 chr1 3800001-6000000 *
#> 3 chr1 6520001-7640000 *
#> 4 chr1 7960001-8920000 *
#> 5 chr1 9240001-9600000 *
#> ... ... ... ...
#> 1886 chrX 148000001-149520000 *
#> 1887 chrX 149840001-150720000 *
#> 1888 chrX 151080001-152920000 *
#> 1889 chrX 152960001-153520000 *
#> 1890 chrX 154560001-156040895 *
#> -------
#> seqinfo: 23 sequences from an unspecified genome; no seqlengthssessionInfo()
#> R Under development (unstable) (2025-03-13 r87965)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.2 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
#>
#> 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
#>
#> 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] MultiAssayExperiment_1.33.9 SummarizedExperiment_1.37.0
#> [3] Biobase_2.67.0 GenomicRanges_1.59.1
#> [5] GenomeInfoDb_1.43.4 IRanges_2.41.3
#> [7] S4Vectors_0.45.4 BiocGenerics_0.53.6
#> [9] generics_0.1.3 MatrixGenerics_1.19.1
#> [11] matrixStats_1.5.0 TENET.ExperimentHub_0.99.3
#> [13] BiocStyle_2.35.0
#>
#> loaded via a namespace (and not attached):
#> [1] KEGGREST_1.47.0 xfun_0.51 bslib_0.9.0
#> [4] lattice_0.22-6 vctrs_0.6.5 tools_4.6.0
#> [7] curl_6.2.1 tibble_3.2.1 AnnotationDbi_1.69.0
#> [10] RSQLite_2.3.9 blob_1.2.4 pkgconfig_2.0.3
#> [13] BiocBaseUtils_1.9.0 Matrix_1.7-3 dbplyr_2.5.0
#> [16] lifecycle_1.0.4 GenomeInfoDbData_1.2.14 compiler_4.6.0
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#> [61] BiocManager_1.30.25 jsonlite_1.9.1 R6_2.6.1