filterSpatialPatterns: Filter for spatial patterns

In JEFworks/MERingue: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with non-uniform cellular densities

Filter for spatial patterns

Description

Filter out spatial patterns driven by small number of cells using LISA

Usage

filterSpatialPatterns(
  mat,
  I,
  w,
  adjustPv = TRUE,
  alpha = 0.05,
  minPercentCells = 0.05,
  verbose = TRUE,
  details = FALSE
)

Arguments

mat	Gene expression matrix.
I	Output of getSpatialPatterns
w	Weight adjacency matrix
adjustPv	Whether to perform BH multiple testing correction
alpha	P-value threshold for LISA score to be considered significant.
minPercentCells	Minimum percent of cells that must be driving spatial pattern
verbose	Verbosity
details	Return details

JEFworks/MERingue documentation built on June 11, 2022, 4:16 a.m.