gene_exp: Gene Expression

In Bishop-Laboratory/RLHub: An ExperimentHub package for accessing processed RLSuite data sets

Description

A SummarizedExperiment containing the gene expression results from RNA-Seq data sets published in tandem with R-loop-mapping data sets.

Usage

gene_exp(quiet = FALSE)

Arguments

quiet

If TRUE, messages are suppressed. Default: FALSE.

Details

Source

For each R-loop-mapping data set in RLBase, any associated RNA-Sequencing data was also downloaded and quantified using salmon v1.4.0. This enables comparison of R-loop abundance and gene expression. The list of SRA accessions from which data was obtained are found here: colData(gene_exp())$sample.

The processing steps are described in the RLBase-data README.md.

Structure

• colData

  • Contains metadata about every sample matching the metadata. See rlbase_samples for a full description.

• assays

  • A SimpleAssays object containing three matrices (genes X samples):

    • cts - Raw read counts

    • tpm - TPM-normalized read counts

    • vst - VST-transformed read counts. (See DESeq2::vst())

Value

A SummarizedExperiment object. See details.

Examples

geneExp <- gene_exp()

Bishop-Laboratory/RLHub documentation built on Jan. 20, 2022, 3:47 p.m.