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PhyloExpressionSet Base Class

Source: R/phyloset_base.R
PhyloExpressionSetBase.Rd

Abstract S7 base class for storing and manipulating phylotranscriptomic expression data. This class provides the common interface for both bulk and single-cell phylotranscriptomic data.

Usage

PhyloExpressionSetBase(
  strata = stop("@strata is required"),
  strata_values = stop("@strata_values is required"),
  expression = stop("@expression is required"),
  groups = stop("@groups is required"),
  name = "Phylo Expression Set",
  species = character(0),
  index_type = "TXI",
  identities_label = "Identities",
  null_conservation_sample_size = 5000L,
  .null_conservation_txis = NULL
)

Arguments

strata

Factor vector of phylostratum assignments for each gene

strata_values

Numeric vector of phylostratum values used in TXI calculations

expression

Matrix of expression counts with genes as rows and samples as columns

groups

Factor vector indicating which identity each sample belongs to

name

Character string naming the dataset (default: "Phylo Expression Set")

species

Character string specifying the species (default: NULL)

index_type

Character string specifying the transcriptomic index type (default: "TXI")

identities_label

Character string labeling the identities (default: "Identities")

null_conservation_sample_size

Numeric value for null conservation sample size (default: 5000)

.null_conservation_txis

Precomputed null conservation TXI values (default: NULL)

Details

The PhyloExpressionSetBase class serves as the foundation for phylotranscriptomic analysis, providing shared functionality for both bulk and single-cell data types.

Abstract Properties: Subclasses must implement the expression_collapsed property to define how expression data should be collapsed across replicates or cells.

Computed Properties: Several properties are computed automatically when accessed:

  • gene_ids - Character vector of gene identifiers (rownames of expression matrix)

  • identities - Character vector of identity labels (colnames of collapsed expression)

  • sample_names - Character vector of sample names (colnames of expression matrix)

  • num_identities - Integer count of unique identities

  • num_samples - Integer count of total samples

  • num_genes - Integer count of genes

  • num_strata - Integer count of phylostrata

  • index_full_name - Full name of the transcriptomic index type

  • group_map - List mapping identity names to sample names

  • TXI - Numeric vector of TXI values for each identity (computed from collapsed expression)

  • TXI_sample - Numeric vector of TXI values for each sample (computed from raw expression)

  • null_conservation_txis - Matrix of null conservation TXI values for statistical testing

Validation: The class ensures consistency between expression data, phylostratum assignments, and groupings. All gene-level vectors must have matching lengths, and sample groupings must be consistent.