Skip to contents

Bulk PhyloExpressionSet Class

Source: R/phyloset_bulk.R
BulkPhyloExpressionSet.Rd

S7 class for bulk RNA-seq phylotranscriptomic expression data. This class handles expression data with biological replicates and provides bootstrapping functionality for statistical analysis.

Usage

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",
  null_conservation_sample_size = 5000L,
  .null_conservation_txis = NULL,
  .bootstrapped_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: "Stages")

null_conservation_sample_size

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

.null_conservation_txis

Precomputed null conservation TXI values (default: NULL)

.bootstrapped_txis

Precomputed bootstrapped TXI values (default: NULL)

Details

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.