getParams: Get parameters used in spatial methods

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Get parameters used in spatial methods

Description

The getParams function allows users to access the parameters used to compute the results that may be stored in colFeatureData.

Usage

getParams(
  sfe,
  name,
  local = FALSE,
  colData = FALSE,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  reducedDimName = NULL
)

Arguments

sfe	A SpatialFeatureExperiment object.
name	Name used to store the results.
local	Logical, whether the results of interest come from a local spatial method.
colData	Logical, whether the results were computed for a column of colData(sfe).
colGeometryName	To get results for a colGeometry.
annotGeometryName	To get results for an annotGeometry; colGeometry has precedence so this argument is ignored if colGeometryName is specified.
reducedDimName	Name of a dimension reduction, can be seen in reducedDimNames. colGeometryName and annotGeometryName have precedence over reducedDimName.

Value

A named list showing the parameters

Examples

library(SFEData)
library(scater)
library(Voyager)
sfe <- McKellarMuscleData("small")
colGraph(sfe, "visium") <- findVisiumGraph(sfe)
sfe <- colDataMoransI(sfe, "nCounts")
getParams(sfe, "moran", colData = TRUE)

pachterlab/SpatialFeatureExperiment documentation built on May 17, 2024, 12:24 a.m.