go_simplify: Simplifies ffsea GO analyses
In facilebio/FacileIncubator: Incubator for half-baked ideas

go_simplify

R 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.