BottomUpMerge: Generate clusterings by iteratively merging two nearest...

In NHLBI-BCB/IKAP: IKAP: Identifying K mAjor cell Population group in single cell analysis

Description

This function generates clusterings by iteratively merging two nearest clusters for a Seurat object. It generates an initial clustering with the number of clusters (k) >= k.max using Seurat SNN clustering. Then iteratively merge two clusters with the nearest centers to generate the clustering with k-1 clusters. Finally, it returns k.max clusterings with k = 1 to k.max.

Usage

BottomUpMerge(sobj, k.max, npc, random.seed)

Arguments

sobj	Seurat object
k.max	the maximal number of clusters
npc	the number of top principal components used for Seurat SNN clustering
random.seed	the random seed set for Seurat SNN clustering

Examples

BottomUpMerge(sobj, k.max, npc, random.seed)

NHLBI-BCB/IKAP documentation built on March 21, 2020, 8:08 p.m.