Seurat
objectR/preprocessing.R
Load10X_Spatial.Rd
Load a 10x Genomics Visium Spatial Experiment into a Seurat
object
Load10X_Spatial( data.dir, filename = "filtered_feature_bc_matrix.h5", assay = "Spatial", slice = "slice1", filter.matrix = TRUE, to.upper = FALSE, ... )
data.dir | Directory containing the H5 file specified by |
---|---|
filename | Name of H5 file containing the feature barcode matrix |
assay | Name of the initial assay |
slice | Name for the stored image of the tissue slice |
filter.matrix | Only keep spots that have been determined to be over tissue |
to.upper | Converts all feature names to upper case. Can be useful when analyses require comparisons between human and mouse gene names for example. |
... | Arguments passed to |
A Seurat
object
if (FALSE) { data_dir <- 'path/to/data/directory' list.files(data_dir) # Should show filtered_feature_bc_matrix.h5 Load10X_Spatial(data.dir = data_dir) }