SpatialStructureDetection: SpatialStructureDetection

In Miaoyx323/stCancer: stCancer

SpatialStructureDetection

Description

Detect spatial structures in the tissue using global and local Morans' I.

Usage

SpatialStructureDetection(
  object,
  feature,
  slice = "slice1",
  global.Moran.I = 0.5,
  p.adjust.method = "fdr",
  p.thres.local = 0.05,
  p.adj.thres.local = 0.05,
  p.thres.z.score = 0.05,
  median.filter = TRUE,
  z.score.filter = TRUE
)

Arguments

object	A Seurat object after stStatistics
feature	The features (genes) of the spatial structure
slice	Slice
global.Moran.I	The threshold for global Morans' I. If the calculated global Morans' I is less than 'global.Moran.I', it is considered that no corresponding spatial structure exists in the tissue
p.adjust.method	The method used to adjust p values
p.thres.local	The threshold for p values of local Morans' I
p.adj.thres.local	The threshold for adjusted p values of local Morans' I
p.thres.z.score	The threshold for z scores of local Morans' I
median.filter	Whether to filter the results using the median of feature scores
z.score.filter	Whether to filter the results based on z-scores
crop	A logical value indicating whether to crop the image during plotting
CNV.ref.object	A reference seurat object used in inferCNV
authorName	A character string for authors name and will be shown in the report.
genReport	A logical value indicating whether to generate a .html/.md report (suggest to set TRUE).

Value

A Seuratobject with results

Miaoyx323/stCancer documentation built on Nov. 14, 2024, 5:31 p.m.