go_simplify: Simplifies ffsea GO analyses

View source: R/go_simplify.R

go_simplifyR Documentation

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.