pruneSSN: Identify and (optionally) prune gene program features in...

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Identify and (optionally) prune gene program features in scale-free shared nearest neighbor network (SSN)

Description

Identify and (optionally) prune gene program features in scale-free shared nearest neighbor network (SSN)

Usage

pruneSSN(object, graph = "RNA_snn_power", prune.threshold = 0.1, return.df = F)

Arguments

object	Seurat object objected from SSN analysis.
graph	name of shared nearest neighbor (SNN) graph used for SSN analysis.
prune.threshold	threshold used for pruning features from SSN graph (features with low connectivity are preferentially pruned). Default is 0.1.
return.df	whether to return data.frame instead of named list.

Value

Returns named list of SSN gene program features.

Author(s)

Nicholas Mikolajewicz

References

https://nmikolajewicz.github.io/scMiko/articles/Module_Detection.html

See Also

runSSN for SSN analysis

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.