runHotspot: Perform Hotspot analysis on Vision Object

In YosefLab/VISION: Functional interpretation of single cell RNA-seq latent manifolds

Perform Hotspot analysis on Vision Object

Description

Perform Hotspot analysis on Vision Object

Usage

runHotspot(
  object,
  model = "normal",
  tree = FALSE,
  number_top_genes = 1000,
  num_umi = NULL,
  min_gene_threshold = 20,
  n_neighbors = NULL,
  autocorrelation_fdr = 0.05,
  clustering_fdr = 0.5,
  logdata = FALSE
)

Arguments

object	Vision Object
model	model argument for Hotspot, one of normal danb bernoulli none
tree	whether to use tree as latent space. If TRUE, object should have a tree slot.
number_top_genes	Hotspot argument for number of genes to consider
num_umi	optional dataframe containing umi counts in first column for barcodes
min_gene_threshold	minimum number of genes in Hotspot module
n_neighbors	number of neighbors to consider in latent space
autocorrelation_fdr	threshold for significance for genes autocorr
clustering_fdr	threshold for significance for clustering modules
logdata	boolean, log the expression data, avoid for danb Populates the modData, HotspotModuleScores, ModuleSignatureEnrichment and HotspotObject slots of object, as well as recalculates signature scores for new modules.

Value

the modified Vision object

YosefLab/VISION documentation built on Feb. 19, 2023, 9:50 p.m.