GECO_score: Score predefined clusters using GECO.

In JasonPBennett/GECO: A metric to determine the biological quality of gene clusters

Description

This function takes a set of user-defined clusters and a set of ground truth genes and scores them using the GECO metric. The gene names within the clusters and the gene names within the ground truth gene sets must match - identical naming conventions must be used for both.

Usage

GECO_score(clusters, gt_dir)

Arguments

clusters	A data.frame with two columns: the first column is the name of a gene and the second is the cluster label/name for that gene.
gt_dir	The absolute path to the directory containing the ground truth gene sets.

Value

A table with two columns: the first column is the name of the ground truth set and the second is the GECO score for that ground truth set.

Examples

# Load clusters
ex_clusters <- clusters_df
# Define ground truth gene set directory
GT_dir <- '/path/to/gt_gene_sets'
# Score the clusters
clusters <- GECO_score(ex_clusters, GT_dir)

JasonPBennett/GECO documentation built on Aug. 30, 2021, 4:30 p.m.