CompassData: CompassData

In YosefLab/compassR: A Library for Conducting Analyses on COMPASS Data

Description

An object through which you can access several useful tables for your COMPASS analysis.

Public fields

settings

The CompassSettings instance specifying the settings for this CompassData instance.

reaction_consistencies

Each row is a reaction and each column is a cell. reaction_consistencies[i, j] is the consitency (or "compatibility") between reaction i and cell j.

metareaction_consistencies

Each row is a metareaction and each column is a cell. metareaction_consistencies[i, j] is the consistency (or "compatibility") between metareaction i and cell j.

metabolic_genes

Each row describes a gene in terms of its ID and whether it's a metabolic gene.

gene_expression_statistics

Each row describes a cell in terms of its ID, total expression, metabolic expression, and metabolic activity.

cell_metadata

The cell metadata from cell_metadata.csv. In this example it's the Th17 cell data from the papers linked above.

gene_metadata

The gene metadata from the metabolic model (RECON2, by default).

metabolite_metadata

The metabolite metadata from the metabolic model (RECON2, by default).

reaction_metadata

The reaction metadata from the metabolic model (RECON2, by default).

reaction_partitions

Each row describes a reaction in terms of its ID, undirected ID, direction, and metareaction ID.

Methods

Public methods

• CompassData$new()

• CompassData$print()

• CompassData$repr()

• CompassData$clone()

---

Method new()

Initialize the CompassSettings instance. Postprocess COMPASS data and populate tables.

Usage

CompassData$new(settings)

Arguments

settings

The CompassSettings instance specifying the settings for this CompassData instance.

Returns

NULL.

---

Method print()

Prints a human-readable representation of this CompassData instance.

Usage

CompassData$print(...)

Arguments

...

Unused.

Returns

NULL.

---

Method repr()

Returns a human-readable representation of this CompassData instance.

Usage

CompassData$repr(...)

Arguments

...

Unused.

Returns

An output.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

CompassData$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

YosefLab/compassR documentation built on May 3, 2021, 7:31 a.m.