Constructor for TSENATAnalysis objects — TSENATAnalysis • TSENAT

Creates a new TSENATAnalysis object with a SummarizedExperiment base and optional initial configuration.

Usage

TSENATAnalysis(se, config = list())

Arguments

se: SummarizedExperiment. The base expression data object.
config: list. Optional initial configuration (usually set via TSENAT_config() instead).

Value

A new TSENATAnalysis object.

Details

The constructor initializes all slots with empty lists except @se, which must be provided. The @metadata slot automatically records: - creation timestamp - TSENAT package version - initial function call

Examples

# Load real TSENAT data
data(readcounts)
metadata_df <- read.table(system.file('extdata', 'metadata.tsv', package
= 'TSENAT'),
  header = TRUE, sep = '\t')
gff3_file <- system.file('extdata', 'annotation.gff3.gz', package = 'TSENAT')
config <- TSENAT_config(sample_col = 'sample', condition_col = 'condition')
analysis <- build_analysis(readcounts = readcounts, tx2gene =
gff3_file, metadata = metadata_df, config = config,
  tpm = tpm, effective_length = effective_length)
analysis <- filter_analysis(analysis, min_samples = 1, subset_n_genes
= 200)