Aggregate Gene Set Scores — aggregate

Function to aggregate geneList based on geneSet, evaluating one geneSet at a time. The function supports multiple aggregation methods as specified by the user.

Usage

aggregate_geneSet(
  geneList,
  geneSet,
  method = c("mean", "median", "meanabs", "meansqr", "maxmean", "ks_orig", "ks_weighted",
    "ks_pos_neg_sum", "sign_test", "rank_sum")
)

Arguments

geneList: A matrix of genes by models, with each column representing a true or null model.
geneSet: A vector containing names of genes in the gene set of interest.
method: A character string specifying the method to use for aggregation. Options include 'mean', 'median', 'meanabs', 'meansqr', 'maxmean', 'sign_test', 'rank_sum', 'ks_orig', 'ks_weighted', 'ks_pos_neg_sum','custom'. Default is 'mean'. If a custom function that takes (genelist, geneSet) as input is provided, this function will use custom aggregation, and set method to 'custom'.

Value

Returns a numeric score based on the specified aggregation method.