Converts a Seurat object into a SummarizedExperiment ready for
logodds_optimized_normFactors.
Usage
prepare_from_seurat(
seurat_obj,
cluster_col,
sample_col,
pheno_cols,
model_formula,
coef_of_interest,
reference_levels = NULL,
random_seed = 42,
unchanged_clusters = NULL,
sanitize_names = TRUE
)Arguments
- seurat_obj
A Seurat object
- cluster_col
Column in meta.data with cluster/cell type labels
- sample_col
Column in meta.data with sample IDs
- pheno_cols
Character vector of columns in meta.data for phenotype data (must be sample-level, not cell-level)
- model_formula
Model formula string (RHS only, e.g., "groupid")
- coef_of_interest
Index or name of coefficient of interest
- reference_levels
Named list: list(variable = reference_level)
- random_seed
Integer random seed
- unchanged_clusters
NULL, or character/integer vector of unchanged clusters
- sanitize_names
Logical, replace spaces/special characters in cluster names (default TRUE)
Value
A SummarizedExperiment ready for logodds_optimized_normFactors