leading_edge_scores: Aggregates gene-level stats from genes in leading edge.

Description Usage Arguments Details Value

View source: R/gsea-utils.R

Description

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.

Usage

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Arguments

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.

Details

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

Value

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.


facilebio/FacileIncubator documentation built on Jan. 14, 2022, 4:57 a.m.