run_goterms: Run GO-Term analysis and retrieve plots This is for usage in...

In paulklemm/mygo: Create Report for mus musculus dataset of GO-term analysis using clusterProfiler

Run GO-Term analysis and retrieve plots This is for usage in custom analysis scripts

Description

Run GO-Term analysis and retrieve plots This is for usage in custom analysis scripts

Usage

run_goterms(
  dat,
  significance_cutoff = 0.05,
  fc_cutoff = 0,
  use_background = FALSE,
  simplify = TRUE,
  simplify_cutoff = 0.7,
  run_kegg = FALSE,
  species = "MUS"
)

Arguments

dat	Table containing ensembl_gene_id, padj and optionally log2FoldChange
significance_cutoff	Adjusted p-value cutoff
fc_cutoff	Fold change cutoff
use_background	Use whole table as gene background
simplify	Summarise GO-terms
simplify_cutoff	When summarising, use this cutoff
run_kegg	Run KEGG pathway analysis. Adds columns kegg and kegg_dt
species	Species string, either "MUS" or "HUM"

Value

list containing plots and table outputs

paulklemm/mygo documentation built on July 27, 2023, 11:36 a.m.