groupGO_all_groups: GO analysis and plots for BP, CC, MF

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Description

This function returns table for GO results for BP, CC, MF with gene symbols. The function may also create excel with the GO result tables and the PDFs with the barplots of the results.

Usage

groupGO_all_groups(
  gene_entrezIDs,
  orgDB,
  name = "",
  bp = 2,
  cc = 3,
  mf = 3,
  xls = TRUE,
  pdf = TRUE
)

Arguments

gene_entrezIDs	vector of entrezIDs
orgDB	db to use for GO
name	name of the output file
bp	level of the biological process with default 2
cc	level of the cellular component with default 3
mf	level of the molecular function with default 3
xls	logical parameter to create excel with with default TRUE
pdf	logical parameter to create pdf with with default TRUE

Value

table with groupGO result arranged as list of dataframes

excel file with groupGO result and the pdf with the groupGO result barplot per biological process, cellular component and molecular function

Examples

groupGO_all_groups(entrez_ids_list, "org.Mmu.eg.db", "out_name", mf = 1, xls = FALSE, pdf = FALSE)

Troshchk/bioEAT documentation built on Dec. 18, 2021, 5:13 p.m.