A SummarizedExperiment containing the gene expression results from RNA-Seq
data sets published in tandem with R-loop-mapping data sets.
gene_exp(quiet = FALSE)
| quiet | If TRUE, messages are suppressed. Default: FALSE. |
|---|
A SummarizedExperiment object. See details.
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.
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())
geneExp <- gene_exp()