S7 class for bulk RNA-seq phylotranscriptomic expression data. This class handles expression data with biological replicates and provides bootstrapping functionality for statistical analysis.
BulkPhyloExpressionSet(
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",
gene_ids = character(0),
null_conservation_sample_size = 5000L,
.null_conservation_txis = NULL,
.bootstrapped_txis = NULL
)A BulkPhyloExpressionSet object
Factor vector of phylostratum assignments for each gene
Numeric vector of phylostratum values used in TXI calculations
Matrix of expression counts with genes as rows and samples as columns
Factor vector indicating which identity each sample belongs to
Character string naming the dataset (default: "Phylo Expression Set")
Character string specifying the species (default: NULL)
Character string specifying the transcriptomic index type (default: "TXI")
Character string labeling the identities (default: "Stages")
Character vector of gene identifiers (default: character(0), auto-generated from expression rownames if not provided)
Numeric value for null conservation sample size (default: 5000)
Precomputed null conservation TXI values (default: NULL)
Precomputed bootstrapped TXI values (default: NULL)
The BulkPhyloExpressionSet class is designed for bulk RNA-seq data with biological replicates. It extends the base PhyloExpressionSetBase class with bulk-specific functionality.
Replicate Handling: Expression data across biological replicates is collapsed by taking row means within each experimental condition or developmental stage.
Computed Properties: In addition to inherited computed properties from the base class, this class provides:
expression_collapsed - Matrix of expression data collapsed across replicates (genes x identities)
bootstrapped_txis - Matrix of bootstrapped TXI values for statistical inference (500 bootstrap samples x identities)
Inherited computed properties from PhyloExpressionSetBase include:
gene_ids - Character vector of gene identifiers
identities - Character vector of identity labels
sample_names - Character vector of sample names
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
TXI_sample - Numeric vector of TXI values for each sample
null_conservation_txis - Matrix of null conservation TXI values for statistical testing
Statistical Analysis: The class supports confidence interval estimation and standard deviation calculation through bootstrapped TXI values, enabling robust statistical analysis of developmental or experimental patterns.