summarize_clusters: Output summary stats from a DIEM run

In marcalva/diem: Debris-Containing Droplet Identification using EM

Output summary stats from a DIEM run

Description

Return summary statistics from a DIEM run to evaluate clustering and classification. The function calculates helpful statistics to evaluate each cluster, including the debris and putatitive cell types. This returns a data frame with the following summary stats per cluster:

Type

Whether the cluster was considered as debris for calculating the debris score.

Cluster

Cluster for which summary stats are shown.

n_droplets

Number of droplets.

avg_n_genes

Average number of genes detected.

avg_n_counts

Average number of counts.

avg_dbr_score

Average debris score, if available.

genes

Set of top top_n marker genes separated by semicolons.

The marker genes are calculated as the genes with the largest difference in proportion between the

Usage

summarize_clusters(x, top_n = 20)

Arguments

x	An SCE object.
top_n	Number of top DE genes to return in column.

Value

A data frame

marcalva/diem documentation built on Jan. 1, 2023, 2:33 a.m.