This function computes summary statistics (nCount and nFeature) for a set of selected genes, useful for creating pathogen-specific metrics.
Usage
GetGeneStat(
STID_obj = NULL,
pattern = NULL,
features = NULL,
prefix = NULL,
func = "sum",
assay_id = "Spatial",
layer_id = "counts"
)Arguments
- STID_obj
A Seurat or STID object
- pattern
Character, regular expression pattern to select genes (default: NULL)
- features
Character vector of specific gene names to include (default: NULL)
- prefix
Character, prefix for output column names
- func
Character, function to apply for nCount calculation. Options: "sum", "mean", "median", "max", "min" (default: "sum")
- assay_id
Character, name of the assay to use (default: "Spatial")
- layer_id
Character, name of the layer/data slot to use (default: "counts")
Value
A data frame with two columns:
- prefix_nCount(func)
Summary statistic for total counts
- prefix_nFeature(sum)
Number of detected features
Examples
if (FALSE) { # \dontrun{
# Calculate pathogen gene statistics
pathogen_stats <- GetGeneStat(
STID_obj = STID_object,
pattern = "^MTB",
prefix = "Pathogen",
func = "sum"
)
# Add to metadata
STID_object <- AddMetaData(STID_object, pathogen_stats)
} # }