This convenience function z-standardizes each feature across samples within an omic and then aggregates features assigned to the same pathway. OmicsBraid's inferential core can also accept externally computed pathway/activity scores, which is recommended when a domain-specific scoring method is preferred.
Usage
score_pathways(
data,
mapping,
method = c("mean_z", "median_z"),
min_features = 3L,
center = TRUE,
scale = TRUE
)Arguments
- data
An `omics_braid_data` object.
- mapping
Data frame with columns `omic`, `feature_id`, and `pathway`.
- method
Aggregation method: `"mean_z"` or `"median_z"`.
- min_features
Minimum mapped features per pathway within an omic.
- center
Logical; center feature values before aggregation.
- scale
Logical; scale feature values before aggregation.