Flag systematic Visium outlier positions

flagVisiumOutliers() marks six Visium array positions that have shown systematically low library sizes across multiple datasets. It accepts either a SpatialExperiment or Seurat object and adds a logical systematic_outliers column to its metadata.

Usage

flagVisiumOutliers(spe, image_id = NULL)

Arguments

spe

A SpatialExperiment or Seurat object containing Visium array coordinates. SpatialExperiment inputs must contain array_row and array_col metadata columns. Seurat inputs may contain the same columns or expose them through a Visium image.

image_id

For Seurat inputs, the image containing Visium array coordinates. The first image is used when NULL.

Value

spe with a logical systematic_outliers metadata column.

Examples

spe <- STexampleData::Visium_humanDLPFC()
#> 
#> see ?STexampleData and browseVignettes('STexampleData') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> 
#> loading from cache
spe <- flagVisiumOutliers(spe)
spe <- spe[, !spe$systematic_outliers]