go_simplify: Simplifies ffsea GO analyses

In facilebio/FacileIncubator: Incubator for half-baked ideas

Simplifies ffsea GO analyses

Description

We use rrvgo, goSemSim and friends

Usage

go_simplify(
  x,
  method = NULL,
  ontology = c("BP", "MF", "CC"),
  direction = c("all", "up", "down"),
  similarity = c("Resnik", "Lin", "Rel", "Jiang", "Wang"),
  threshold = 0.7,
  max_padj = 0.1,
  min_logFC = NULL,
  score_by = NULL,
  semdata = NULL,
  ...,
  verbose = FALSE
)

Arguments

x	A FacileFseaAnalysisResult
ontology	which ontology are were summarizing? BP, MF, or CC
direction	focus on all genes, or only up or down regulated genes (works for ttest, not ANOVA)
similarity	The method to use to measure similarity, see here.
min_logFC, max_padj	parameters used to define signficant genes. If the TREAT framework was used, defaults to the threshold tested, otherwise its zero.

facilebio/FacileIncubator documentation built on Sept. 19, 2024, 8:06 p.m.