IsoformicExperiment Class — IsoformicExperiment • isoformic

The IsoformicExperiment class encapsulates the core data structure for transcriptomic analyses in the isoformic package. It holds the path to the dataset, sample metadata, and provides access to transcript, gene, and exon annotations through properties. The preferred way to construct an object of this class is through the IsoformicExperiment() constructor.

Usage

IsoformicExperiment(
  experiment_name = NA_character_,
  data_path = NULL,
  annot_path = NULL,
  assay = NULL,
  col_data = NULL,
  annot_metadata = NULL,
  dea = NULL,
  gsea = NULL,
  tx_type_palette = character(0)
)

col_data(self, ...)

annot_data_transcripts(self, ...)

annot_data_genes(self, ...)

annot_data_exons(self, ...)

annot_data(self, ...)

annot_row_names(self, ...)

col_names(self, ...)

row_names(self, ...)

tx_to_gene(self, ...)

tx_annot(self, ...)

de_tx(self, ...)

de_gene(self, ...)

Arguments

experiment_name: Character string specifying the name of the experiment. This name is used for caching the assays experiment. If a name is not provided a random identifier is used.
data_path: Character string specifying the path to the data directory.
annot_path: Character string specifying the path to the annotation database directory.
assay: A list of matrices or data frames containing assay data, with transcript IDs as row names and sample IDs as column names. Each element of the list represents a different assay (e.g., TPM, counts).
col_data: A data frame containing sample metadata. First column must be sample_id matching the column names of the assays.
annot_metadata: A list containing metadata about the annotation, such as source, version, and date.
dea: A list containing differential expression analysis results for transcripts and genes.
gsea: A list containing gene set enrichment analysis results.
tx_type_palette: A named character vector specifying the color palette for different transcript types.
self: An IsoformicExperiment object.
...: Additional arguments passed to methods.
annot_data_transcripts: A property that retrieves transcript annotation data.
annot_data_genes: A property that retrieves gene annotation data.
annot_data_exons: A property that retrieves exon annotation data.
annot_data: A property that aggregates transcript, gene, and exon annotation data.