create.SpaCET.object.10X: Create an SpaCET object from 10X Visium

In data2intelligence/SpaCE: Spatial Cellular Estimator for Tumors

Create an SpaCET object from 10X Visium

Description

Read an ST dataset to create an SpaCET object.

Usage

create.SpaCET.object.10X(visiumPath)

Arguments

visiumPath

Path to the Space Ranger output folder. See ‘details’ for more information.

Details

If users are analyzing an ST data set from 10X Visium platform, they only need to input "visiumPath". Please make sure that "visiumPath" points to the standard output folder of 10X Space Ranger, which has both (1) sequencing data, i.e., 'filtered_feature_bc_matrix.h5' file or 'filtered_feature_bc_matrix' folder,

The "filtered_feature_bc_matrix" folder includes
"barcodes.tsv.gz": spot level barcodes;
"features.tsv.gz": list of genes;
"matrix.mtx.gz": (sparse) matrix of counts.

and (2) image folder 'spatial'.

The "spatial" folder includes
“tissue_positions_list.csv” : barcodes and spatial information;
“tissue_lowres_image.png” : hematoxylin and eosin (H&E) image;
“scalefactors_json.json” : scaling factors for adjusting the coordinates.

Value

An SpaCET object.

Examples

visiumPath <- file.path(system.file(package = "SpaCET"), "extdata/Visium_BC")
SpaCET_obj <- create.SpaCET.object.10X(visiumPath = visiumPath)

data2intelligence/SpaCE documentation built on Dec. 20, 2024, 1:41 a.m.