find_low_quality_cl: Use DEGenes to identify clusters with few differentially...

In AllenInstitute/scrattch.hicat: Hierarchical Iterative Clustering Analysis for Transcriptomic data

Use DEGenes to identify clusters with few differentially expressed genes

Description

To use this, you'll need to perform pairwise gene expression tests with de_score(), and a set of clusters with high confidence (cl.good).

Usage

find_low_quality_cl(cl.df, cl.good, de.score.mat = NULL, de.genes)

Arguments

cl.df	A data.frame with cluster annotations that includes a "cluster_label" column
cl.good	a cluster factor object for cells from high-quality clusters.
de.genes	differential gene expression results like those generated by de_score().

Details

Low-quality clusters will be from all clusters in cl.df that are not in cl.good.

Value

a data.frame with the closest "good" cluster for each non-good/low cluster.

AllenInstitute/scrattch.hicat documentation built on Oct. 20, 2023, 6:55 a.m.