read_enrich_tables: Read enrichment results from tables

In isabellagrassucci/autoGO: Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations

Read enrichment results from tables

Description

Helper function to read all the enrichment results in order to proceed with the visualization in an automated way.

Usage

read_enrich_tables(
  where_results = "./",
  outfolder = "results/",
  log2FC_threshold = 0,
  padj_threshold = 0.05,
  which_list = c("up_genes", "down_genes", "up_down_genes", "everything"),
  from_DE_analysis = T,
  where_files = NULL,
  files_format = NULL
)

Arguments

where_results	Specify the folder in which you want to save the outputs. Default is "./". Note: if you are working with RNotebook the default working directory, if not specified, is the folder in which the .Rmd file is saved.
outfolder	The name to assign to the folder for output saving. (Default = "results/"). NOTE: please add "/" at the end.
log2FC_threshold	Threshold value for log2(Fold Change) for considering genes as differentially expressed (default = 0).
padj_threshold	Threshold value for adjusted p-value significance (Defaults to 0.05).
which_list	One of c("up_genes","down_genes","up_down_genes","everything"). Select a list of genes to perform the enrichment. Respectively, only up regulated genes (up_genes), only down regulated genes (down_genes), both up and down regulated genes (up_down_genes), or everything allow to load all the three kind of lists separately.
from_DE_analysis	Default is TRUE, set to FALSE if the lists you want to upload are not from a differential expression analysis.
where_files	Default is NULL, when from_DE_analysis = T it is mandatory to provide a path to specify where the list of genes are.
files_format	Default is NULL, when from_DE_analysis = T it is mandatory to provide the extension of the list of genes you want to upload.

isabellagrassucci/autoGO documentation built on April 5, 2022, 7:49 p.m.