| Title: | Reference Perturbation Signatures from GEO RNA-seq Experiments |
|---|---|
| Description: | Provides the reference perturbation expression signatures used by the perturbMatch package, which ranks the single-gene perturbations whose expression response most resembles a query signature. Each reference signature summarises the differential expression observed after a single-gene perturbation (knockdown, knockout or overexpression) in a human RNA-seq experiment deposited in the Gene Expression Omnibus. Signatures are summarised either by the characteristic direction method or by limma, each with and without surrogate variable analysis batch correction, giving four datasets served as HDF5-backed SummarizedExperiment objects. |
| Authors: | Jamie Soul [aut, cre] (ORCID: <https://orcid.org/0000-0003-2255-6459>), Versus Arthritis [fnd] |
| Maintainer: | Jamie Soul <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.99.0 |
| Built: | 2026-09-21 11:34:54 UTC |
| Source: | https://github.com/BiocStaging/perturbMatchData |
Returns the ExperimentHub records prepared by this package. This is a way to inspect what is hosted and what is already cached locally. To work with the data, use the dataset accessors described in perturbMatchReferenceData, which assemble the records into a SummarizedExperiment for you.
perturbMatch_reference()perturbMatch_reference()
An ExperimentHub subset of the perturbMatchData records.
perturbMatchReferenceData for the dataset accessors.
perturbMatch_reference()perturbMatch_reference()
Retrieve one of the perturbMatch reference expression databases as an HDF5-backed SummarizedExperiment. The assays stay in the ExperimentHub cache and are read from disk on demand.
perturbMatch_chrdir(withAssays = TRUE) perturbMatch_chrdir_sva(withAssays = TRUE) perturbMatch_limma(withAssays = TRUE) perturbMatch_limma_sva(withAssays = TRUE)perturbMatch_chrdir(withAssays = TRUE) perturbMatch_chrdir_sva(withAssays = TRUE) perturbMatch_limma(withAssays = TRUE) perturbMatch_limma_sva(withAssays = TRUE)
withAssays |
Whether the returned object carries the assay data. With
|
perturbMatch_chrdirCharacteristic direction signatures.
perturbMatch_chrdir_svaCharacteristic direction, SVA batch-corrected.
perturbMatch_limmalimma log2 fold-change / pi-score signatures.
perturbMatch_limma_svalimma signatures, SVA batch-corrected.
All four are derived from GEO RNA-seq experiments and share a 39,376-gene space, and so also share one gene annotation resource.
The signature matrices are large: 790 MB for chrdir and 673 MB for
chrdir_sva, and 3.1 GB and 2.6 GB for limma and
limma_sva, which carry three assays each. They are downloaded once
and then read from the ExperimentHub cache.
A SummarizedExperiment with HDF5-backed assays.
## which perturbations are available, without the assay data. Only the ## annotation resources are downloaded, a few MB rather than gigabytes se <- perturbMatch_chrdir(withAssays = FALSE) head(SummarizedExperiment::colData(se)) ## the full dataset, 790 MB of signature matrices on first use se <- perturbMatch_chrdir() SummarizedExperiment::assay(se)[1:5, 1:3]## which perturbations are available, without the assay data. Only the ## annotation resources are downloaded, a few MB rather than gigabytes se <- perturbMatch_chrdir(withAssays = FALSE) head(SummarizedExperiment::colData(se)) ## the full dataset, 790 MB of signature matrices on first use se <- perturbMatch_chrdir() SummarizedExperiment::assay(se)[1:5, 1:3]