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Get parameters used in spatial methods

Source: R/featureData.R
getParams.Rd

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)
sfe <- McKellarMuscleData("small")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
colGraph(sfe, "visium") <- findVisiumGraph(sfe)
sfe <- colDataMoransI(sfe, "nCounts")
getParams(sfe, "moran", colData = TRUE)
#> $name
#> [1] "moran"
#> 
#> $package
#> [1] "spdep"
#> 
#> $version
#> [1] ‘1.3.1’
#> 
#> $zero.policy
#> NULL
#> 
#> $include_self
#> [1] FALSE
#> 
#> $graph_params
#> $graph_params$FUN
#> [1] "findVisiumGraph"
#> 
#> $graph_params$package
#> $graph_params$package[[1]]
#> [1] "SpatialFeatureExperiment"
#> 
#> $graph_params$package[[2]]
#> [1] ‘1.3.0’
#> 
#> 
#> $graph_params$args
#> $graph_params$args$style
#> [1] "W"
#> 
#> $graph_params$args$zero.policy
#> NULL
#> 
#> $graph_params$args$sample_id
#> [1] "Vis5A"
#> 
#> 
#>