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SEStats S7 Object

Source: R/jam_sestats_class.R
SEStats.Rd

S7 object for storing statistical results from comparative analysis.

Usage

SEStats(
  sedesign = NULL,
  stats_dfs = list(),
  stats_objects = list(),
  hit_array = NULL,
  metadata = list()
)

Details

The SEStats object is an S7 class designed to store comprehensive statistical results from differential analysis on SummarizedExperiment data. It maintains relationships between the experimental design, statistical results at different cutoff thresholds, and a 3-dimensional hit array that summarizes significant findings across multiple dimensions.

The hit_array is the central data structure, a 3-dimensional array where:

  • Cutoffs are derived from column names in each data.frame of stats_dfs (columns beginning with "hit ")

  • Contrasts are the names within each stats_dfs element

  • Signal values are the top-level names in stats_dfs

The dimensions should satisfy these relationships:

  • All Signal values in hit_array should appear in names(stats_dfs)

  • All Contrast values should appear in names(stats_dfs[[signal]]) for at least one signal

  • Cutoff names are extracted from data.frame column names

Slots

sedesign

SEDesign object containing the experimental design and contrast information.

stats_dfs

nested list structure organizing data.frame of statistical results. The structure is stats_dfs[[signal]][[contrast]] where each data.frame contains detailed statistical metrics for a specific signal type (assay) and contrast comparison.

stats_objects

An optional list for storing raw statistical objects or intermediate result objects used to generate stats_dfs. Currently unused but provided for future extensibility.

hit_array

A 3-dimensional array with dimnames:

  • Dimension 1 (Cutoffs): Statistical threshold variations

  • Dimension 2 (Contrasts): Comparison between sample groups

  • Dimension 3 (Signal): Different assay names/normalization methods Cell values are named numeric vectors indicating hit status.

metadata

An optional list containing analysis parameters and metadata associated with the statistical analysis.

See also

Other SEStats objects: contrast_names,SEStats-method, factors,SEStats-method, groups,SEStats-method, print,SEStats-method, samples,SEStats-method