Package 'CLAMPData'

Title: Experiment data for CLAMP package
Description: Curated CLAMP resources (latent variables, loadings, priors, and example matrices) for use with the CLAMP package, distributed via ExperimentHub.
Authors: Marc Subirana-Granés [aut, cre] (ORCID: <https://orcid.org/0000-0003-3934-839X>)
Maintainer: Marc Subirana-Granés <[email protected]>
License: MIT + file LICENSE
Version: 0.99.5
Built: 2026-10-10 10:47:17 UTC
Source: https://github.com/bioc/CLAMPData

Help Index

Expected HDF5 schema for CLAMP expression files

Description

Returns a data frame of the paths, types, and purpose of each dataset required in a CLAMP HDF5 expression file.

Usage

clamp_h5_schema()

Value

A data frame with columns path, type, and description.

Examples

clamp_h5_schema()

GSE164416_DP_htseq_counts_txt_gz

Description

Retrieves the raw count matrix (path to gzipped file) for the GSE164416 dataset from ExperimentHub.

Usage

GSE164416_DP_htseq_counts_txt_gz()

Value

A character string representing the local file path to the downloaded resource.

Examples

if (interactive()) {
    counts_path <- GSE164416_DP_htseq_counts_txt_gz()
    print(counts_path)
}

human_gene_v2_5_alz_h5

Description

Retrieves the H5 file (path) containing gene sets and pathway priors from ExperimentHub.

Usage

human_gene_v2_5_alz_h5()

Value

A character string representing the local file path to the downloaded resource.

Examples

if (interactive()) {
    h5_path <- human_gene_v2_5_alz_h5()
    print(h5_path)
}

islets_metadata_csv

Description

Retrieves the metadata CSV file (path) for the islets example from ExperimentHub.

Usage

islets_metadata_csv()

Value

A character string representing the local file path to the downloaded resource.

Examples

if (interactive()) {
    metadata_path <- islets_metadata_csv()
    print(metadata_path)
}

List available CLAMPData datasets

Description

Returns a data frame of all datasets in the package, one row per resource. The accessor column names the function that returns the local file path for each resource.

Usage

list_clamp_data()

Value

A data.frame with columns name, accessor, description, type, species, eh_id, and version.

Examples

datasets <- list_clamp_data()
datasets[, c("name", "type", "eh_id")]

Load the Alzheimer expression matrix

Description

Downloads the Alzheimer HDF5 file via ExperimentHub, validates it against clamp_h5_schema, and returns the expression matrix oriented as genes x samples with gene symbols and sample identifiers as row and column names

Usage

read_clamp_alz_expression()

Value

A numeric matrix with gene symbols as row names and sample identifiers as column names.

Examples

if (interactive()) {
    expr <- read_clamp_alz_expression()
    dim(expr)
}

Load islet count table

Description

Downloads the GSE164416 HTSeq count file via ExperimentHub and reads it as a data frame

Usage

read_islet_counts()

Value

A data frame with an ensembl gene-ID column and one count column per sample.

Examples

if (interactive()) {
    counts <- read_islet_counts()
    dim(counts)
}

Load islet sample metadata

Description

Downloads the islet sample metadata CSV via ExperimentHub and reads it as a data frame

Usage

read_islet_metadata()

Value

A data frame with one row per sample.

Examples

if (interactive()) {
    meta <- read_islet_metadata()
    head(meta)
}

Validate a CLAMP HDF5 file

Description

Checks that an HDF5 file contains the datasets CLAMP expects (see clamp_h5_schema).

Usage

validate_clamp_h5(path)

Arguments

path

Path to an HDF5 file.

Value

TRUE invisibly if the file is valid; otherwise stops with a message listing the missing datasets.

Examples

if (interactive()) {
    validate_clamp_h5(human_gene_v2_5_alz_h5())
}