SCORPION (version 1.3.3)

scorpionTest: Example single-cell colorectal cancer data for SCORPION

Description

A list bundling the inputs required to build and compare gene regulatory networks with SCORPION, derived from a colorectal cancer single-cell RNA-sequencing experiment. It contains a gene expression matrix, a transcription factor motif prior, a protein-protein interaction prior, and cell-level metadata.

Usage

data(scorpionTest)

Format

A named list with four elements:

gex

A dgCMatrix gene expression matrix with 300 genes (rows) and 1,954 cells (columns).

tf

A data.frame of transcription factor-target motif pairs from DoRothEA with columns source_genesymbol, target_genesymbol and weight (371,738 rows).

ppi

A data.frame of protein-protein interactions with columns source_genesymbol, target_genesymbol and weight (4,076 rows).

metadata

A data.frame of cell-level annotations with columns cell_id, donor, region and cell_type (1,954 rows). Region codes are T (tumor), B (border) and N (normal).

Examples

# Loading example data
data(scorpionTest)

# The structure of the data
str(scorpionTest)