Uses a symbol-based expression matrix derived from expr_anno and a
user-supplied gene set database.
Usage
run_signature_analysis(
expr_anno,
geneset_file = NULL,
gene_sets = NULL,
method = c("gsva", "ssgsea", "both"),
gene_column = "symbol",
expr_scale = c("auto", "count", "abundance", "log"),
duplicate_strategy = c("auto", "sum", "mean", "max", "first"),
kcdf = c("auto", "Gaussian", "Poisson", "none"),
min_size = 1,
max_size = Inf,
gsva_args = list(),
ssgsea_args = list(),
output_dir = NULL,
prefix = "signature_"
)Arguments
- expr_anno
Annotated expression table.
- geneset_file
Optional GMT path.
- gene_sets
Optional named list of gene sets.
- method
One of
"gsva","ssgsea", or"both".- gene_column
Symbol column to use.
- expr_scale
Expression scale. This affects duplicate symbol handling.
- duplicate_strategy
Strategy used when multiple rows map to the same symbol.
"auto"uses"sum"for counts and"mean"otherwise.- kcdf
Kernel choice passed to
GSVA::gsvaParam().- min_size
Minimum gene-set size after ID matching.
- max_size
Maximum gene-set size after ID matching.
- gsva_args
Optional named list of extra arguments passed to
GSVA::gsvaParam().- ssgsea_args
Optional named list of extra arguments passed to
GSVA::ssgseaParam().- output_dir
Optional output directory.
- prefix
File prefix.