Converts a Seurat object to an STID (Integrated Single-cell Transcriptomics) object, adding infection-specific metadata and analysis structures.
Usage
as.STID(seurat_obj, ...)
# S4 method for class 'Seurat'
as.STID(
seurat_obj = NULL,
host_org = NULL,
pathogen_grp = NULL,
pathogen_org = NULL,
samp_colnm = NULL,
samp_grp_colnm = NULL,
celltype_colnm = NULL,
x_colnm = NULL,
y_colnm = NULL,
pathogen_genes = NULL,
data_format = NULL,
data_platform = NULL,
binsize = NULL,
coord_interval = NULL,
base_unit = NULL,
project_id = NULL,
description = NULL,
...
)Arguments
- seurat_obj
A Seurat object to be converted
- ...
Additional arguments passed to methods
- host_org
Character, host organism - "human", "mouse", or "unknown"
- pathogen_grp
Character, pathogen group - "virus", "bacteria", "parasite", or "unknown"
- pathogen_org
Character, specific pathogen organism name
- samp_colnm
Character, column name in metadata containing sample IDs
- samp_grp_colnm
Character, column name in metadata containing sample groups
- celltype_colnm
Character, column name in metadata containing cell types
- x_colnm
Character, column name for x coordinates
- y_colnm
Character, column name for y coordinates
- pathogen_genes
Character vector, names of pathogen genes
- data_format
Character, data format - "square_grid" or "hex_grid"
- data_platform
Character, data platform - "StereoSeq", "Visium", "VisiumHD", "SlideSeq", or "unknown"
- binsize
Numeric, bin size for spatial data
- coord_interval
Numeric, coordinate coord_interval
- base_unit
Numeric, base unit for spatial coordinates, and the unit is mm
- project_id
Character, project identifier
- description
Character, project description
Value
An STID object containing the converted data with infection-specific metadata and analysis structures
Examples
if (FALSE) { # \dontrun{
# Convert Seurat object to STID object
ist_obj <- as.STID(
seurat_obj = seurat_object,
samp_colnm = "sample_id",
celltype_colnm = "cell_type",
host_org = "human",
pathogen_grp = "virus",
pathogen_org = "SARS-CoV-2",
data_format = "square_grid",
data_platform = "StereoSeq",
binsize = 1,
coord_interval = 1,
base_unit = 0.5,
project_id = "STID_Project_001",
description = "This is a test project for converting Seurat to STID."
)
} # }