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Load the 10x Human Lymph Node Visium dataset as a Seurat object

Source: R/io-seurat.R
load_10x_lymphnode.Rd

This loader is tailored to the authoritative MVP assets: V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5, V1_Human_Lymph_Node_spatial.tar.gz, and V1_Human_Lymph_Node_metrics_summary.csv.

Usage

load_10x_lymphnode(
  data_dir = ".",
  h5_file = "V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5",
  spatial_tar = "V1_Human_Lymph_Node_spatial.tar.gz",
  metrics_file = "V1_Human_Lymph_Node_metrics_summary.csv",
  assay = "Spatial",
  slice = "slice1",
  filter.matrix = TRUE
)

Arguments

data_dir

Directory containing the raw files.

h5_file

Name of the feature-barcode H5 file.

spatial_tar

Name of the spatial tar.gz archive.

metrics_file

Name of the metrics CSV file.

assay

Assay name passed to Seurat::Load10X_Spatial().

slice

Slice name passed to Seurat::Load10X_Spatial().

filter.matrix

Logical; forwarded to Seurat::Load10X_Spatial().

Value

A Seurat spatial object.

Details

It will unpack the spatial tarball automatically when spatial/ is missing, then call Seurat::Load10X_Spatial().