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The SingleSampNiche Class

Source: R/STID-class.R
SingleSampNiche-class.Rd

A container for niche analysis results from a single sample. Stores information about detected niches, including their spatial coordinates, associated cells, and gene expression patterns.

Slots

samp_info

List containing sample information:

  • samp_id: Character, sample identifier

niche_info

Data frame containing metadata for each niche:

  • niche_key: Character, unique identifier for the niche

  • meta_key: Character, reference to metadata source

  • ROI_type: Character, type of ROI ("ROI", "Spot", or "Unknown")

  • pos_colnm: Character, column name for positive spot labels

  • center_colnm: Character, column name for center spot labels

  • edge_colnm: Character, column name for edge spot labels

  • all_label_colnm: Character, column name for all spot labels

  • all_dist_colnm: Character, column name for distance to center

  • niche_cells_num: Integer, number of cells in the niche

  • niche_genes_num: Integer, number of genes analyzed

  • description: Character, description of the niche

niche_cells

List containing data frames of cell-level information for each niche key

niche_genes

List containing data frames of gene-level information for each niche key

See also

Other niche-classes: MultiSampNiche-class