Package 'TumourMethData'

Title: A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples
Description: TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies.
Authors: Richard Heery [aut, cre] (ORCID: <https://orcid.org/0000-0001-8067-3114>)
Maintainer: Richard Heery <[email protected]>
License: Artistic-2.0
Version: 1.11.0
Built: 2026-10-10 11:18:36 UTC
Source: https://github.com/bioc/TumourMethData

Help Index

TumourMethData: A collection of DNA methylation datasets for human tumour samples and matching normal samples

Description

TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments, facilitating easy extraction of methylation data for regions of interest. At present, includes the following datasets:

Details

  • cpgea_wgbs_hg38: WGBS Data from 187 pairs of matching human prostate tumours and normal prostate samples.

  • tcga_wgbs_hg38: WGBS Data from 39 bladder, breast, colon, glioblastoma, lung, rectal stomach and uterine tumour samples and and 8 matching normal samples.

  • mcrpc_wgbs_hg38: WGBS data from 100 prostate cancer metastases.

  • mcrpc_wgbs_hg38_chr11: Subset of mcrpc_wgbs_hg38 with methylation values for just chromosome 11.

  • cao_esophageal_wgbs_hg19: WGBS data for 10 squamous esophageal tumours and 9 matching normal samples.

  • target_rhabdoid_wgbs_hg19: WGBS data for 69 childhood rhabdoid tumours.

Author(s)

Richard Heery

See Also

Useful links:

Download a WGBS methylation dataset from TumourMethData

Description

The HDF5 file and RDS file to construct a RangedSummarizedExperiment for the specified dataset are downloaded into the ExperimentHub cache located at ExperimentHub::getExperimentHubOption("cache"). A copy of the RDS file pointing to the HDF5 file in the cache is saved in the specified directory.

Usage

download_meth_dataset(dataset, dir = getwd())

Arguments

dataset

Name of the dataset to download WGBS data from. Must be one of the datsets listed in data(TumourMethDatasets).
dir

Directory in which to save a the copy of the RDS file pointing to the location of the HDF5 file in the ExperimentHub cache. Default is the current directory.

Value

A RangedSummarizedExperiment with methylation values from the specified dataset.

Examples

mcrpc_wgbs_hg38_chr11 = TumourMethData::download_meth_dataset(dataset = "mcrpc_wgbs_hg38_chr11")
print(mcrpc_wgbs_hg38_chr11)

Download a RNA-Seq counts dataset from TumourMethData

Description

Download a RNA-Seq counts dataset from TumourMethData

Usage

download_rnaseq_dataset(dataset)

Arguments

dataset

Name of the dataset to download. Must be one of the datasets listed in data(TumourMethDatasets) where transcript_counts_available is TRUE.

Value

A data.frame with RNA-Seq counts calcualted using Kallisto.

Examples

mcrpc_rnaseq = TumourMethData::download_rnaseq_dataset(dataset = "mcrpc_wgbs_hg38_chr11")
print(mcrpc_rnaseq)

TumourMethDatasets

Description

A table describing the datasets available from TumourMethData.

Usage

TumourMethDatasets

Format

A data.frame with one row for each dataset