S7 class for bulk RNA-seq phylotranscriptomic expression data. This class handles expression data with biological replicates.
Usage
BulkPhyloExpressionSet(
strata = stop("@strata is required"),
strata_values = stop("@strata_values is required"),
gene_ids = stop("@gene_ids is required"),
name = "Phylo Expression Set",
species = character(0),
index_type = "TXI",
identities_label = "Identities",
null_conservation_sample_size = 5000L,
precomputed_null_conservation_txis = NULL,
.expression = stop("@.expression is required"),
.groups = stop("@.groups is required"),
precomputed_bootstrapped_txis = NULL
)Arguments
- strata
Factor vector of phylostratum assignments for each gene
- strata_values
Numeric vector of phylostratum values used in TXI calculations
- gene_ids
Character vector of gene identifiers
- 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)
- precomputed_null_conservation_txis
Precomputed null conservation TXI values (default: NULL)
- .expression
Matrix of expression counts with genes as rows and samples as columns
- .groups
Factor vector indicating which identity each sample belongs to
- precomputed_bootstrapped_txis
Precomputed bootstrapped TXI values (default: NULL)