Calculate Niche Gene Expression Correlations

Computes correlation between pathogen and host gene expression within niches. Supports both feature-based and gene-based correlation analysis.

Usage

CalSampGeneCor(
  STID_obj = NULL,
  loop_id = "LoopAllSamp",
  meta_key = NULL,
  niche_key = NULL,
  p.features = NULL,
  h.features = NULL,
  p.feature_colnm = NULL,
  h.feature_colnm = NULL,
  method = "spearman",
  assay_id = "Spatial",
  layer_id = "data",
  return_data = TRUE,
  grp_nm = NULL,
  dir_nm = "M3_CalSampGeneCor"
)

Arguments

STID_obj: An STID object containing niche analysis results
loop_id: Character, sample grouping identifier (default: "LoopAllSamp")
meta_key: Character, metadata key for analysis when niche_key is NULL
niche_key: Character, niche key to analyze
p.features: Character vector, pathogen gene names
h.features: Character vector, host gene names
p.feature_colnm: Character vector, pathogen feature column names in metadata
h.feature_colnm: Character vector, host feature column names in metadata
method: Character, correlation method - "spearman" or "pearson" (default: "spearman")
assay_id: Character, assay name (default: "Spatial")
layer_id: Character, layer name (default: "data")
return_data: Logical, whether to return results list (default: TRUE)
grp_nm: Character, group name for output organization (default: NULL)
dir_nm: Character, directory name for output (default: "M3_CalSampGeneCor")

Value

If return_data = TRUE, returns a list of correlation results per sample

Examples

if (FALSE) { # \dontrun{
# Correlate pathogen and host gene expression
results <- CalSampGeneCor(
  STID_obj = STID_obj,
  niche_key = "niche_virulence",
  p.features = c("pathogen_gene1", "pathogen_gene2"),
  h.features = c("host_gene1", "host_gene2"),
  method = "spearman"
)
} # }