The Matchmaker S4 Class

The Matchmaker object with the slot information listed as follow:

Slots

data

Expression data. A d x M matrix with d rows of interaction genes and M columns of data points (cells).

annotation

Data frame of cell type annotatiuons.

• first column, stores the cell type identities for each cell in the data.

• ..., additional slots for future use.

interaction

Ligand-receptor interaction pairs. A dataframe with at least two columns for ligand-receptor pair gene names.

strength

Matrix of relative strengths of interactions.

• row names, interacting cell types seperated by "|".

• column names, interacting partner pairs seperated by "_".

pvalue

Matrix of p values of interaction strengths. Row and column naming are the same as the strength matrix.

selected

A list of selected and filtered interactions:

• stregth, Matrix of relative strengths of interactions.

• pvalue, Matrix of p values of interaction strengths.

• merged.data, merged interaction pair data and strength data.

project_name

Name of the project.

misc

List of miscellaneous:

• raw_data, raw expression data.

• stats_null, null interaction stength without earth mover's distance adjustment if emd=TRUE option is used.

• emd, earth mover's distance similarity.

• permute_result, list of permutation results if saved.

• sketch_id, geometric sketching ID.

• graph, graph visualization.

• single_interaction, single gene-gene interaction table in the format of single interactions if Complexing function is called.

• single_strength, single gene-gene interaction strengths if Complexing function is called.

• single_pvalue, single gene-gene interaction p-values of interactions strengths if Complexing function is called.

• unmerged_strength, unmerged interaction strenghts if Merging function is called.

• unmerged_pvalue, unmerged interaction p-values if Merging function is called.

• ..., additional slots for future use.

command

Nested list of commands and scMatchmaker version used.