leading_edge_scores: Aggregates gene-level stats from genes in leading edge.
In facilebio/FacileIncubator: Incubator for half-baked ideas

Description Usage Arguments Details Value

View source: R/gsea-utils.R

The logFC and t-statistics of the genes from the leading edge (defined in extract_leading_edge()) are used to give an effect size of the geneset shift.

leading_edge_scores(
  x,
  leading_edge = NULL,
  aggregate = c("t", "logFC"),
  stats = NULL,
  ...
)

`x`	The FacileFseaAnalysisResult objects where `fgsea` was ran.
`leading_edge`	Precaculated leading edge genes, as in the output from `leading_edge()`. If `NULL`, the leading_edge will be caluclated for all genesets tested `x` then scored. The scoring can take a long time if there are many, so you may want to provide a filtered leading_edge set.
`aggregate`	the column names from the dge results to summarize, defaults to `c("t", "logFC")`
`stats`	A name of a gsea method run in `"x"` to append pvalues from. If `NULL` (default), none will be added.

This is used in place of the ES/NES mojo.

a tibble of geneset scores, aggregated by leading edge genesets for columns in aggregate. If "fgsea" is a method run in "x", ES, and NES columns will be returned as well.