s4_gene_enrichment_analysis: s4 gene enrichment analysis

In galelab/GaleGEAnalysis: What the Package Does (One Line, Title Case)

Description

This function runs gene enrichment analysis

Usage

s4_gene_enrichment_analysis(
  go_enrich_type = "BP",
  universe = TRUE,
  universe_file = " ./s1_raw_counts_results/1.norm_matrix_HGNC.txt",
  DEgenes = FALSE,
  log_values_column = FALSE,
  rnkfile = FALSE,
  results_folder = "s4_gene_enrichment_results",
  comparison = FALSE,
  modules = TRUE,
  module_results_folder = "s3_DE_results",
  NumTopGoTerms = 30,
  figres = 300,
  ensembl_retrieve = TRUE,
  gene_name_type = "SYMBOL",
  base_file_name = "ge.png"
)

Arguments

go_enrich_type	type of GO enrichment to do (BP, CC, or MF) (default BP)
universe	Will specify whether you want to use the whole genome as background (FALSE) or set of total expressed genes(TRUE)
universe_file	specifies path to universe file(defualt ./s1_raw_counts_results/1.norm_matrix_HGNC.txt)
DEgenes	file containg log fold change for DE genes (default FALSE, needs to be given with log_values_column if used)
rnkfile	file containing list of users own genes (not generated in step s3). Must be in rank file format (gene name & logfold value seperated by tab)
results_folder	user specified output folder (default is s4_gene_enrichment_results)
comparison	specify name of time point comparison to perform over enrichment analysis
modules	perform over enrichment analysis on modules generated in step s3
module_results_folder	folder where DE results are (default s3_DE_results/)
NumTopGoTerms	top GO terms to show (default 10)
figres	resolution of output figures (default 300)
ensembl_retrieve	whether or not to retrieve gene name descriptions
base_file_name	name to save files under (default ge.png)
log_fold_column	column to pull from DEgenes

Examples

s4_gene_enrichment_analysis(DEgenes=FALSE, go_enrich_type="BP", log_values_column=FALSE, modules=TRUE, pvalue=0.05, qvalue=0.05, NumTopGoTerms=30)

galelab/GaleGEAnalysis documentation built on May 18, 2020, 7:32 a.m.