read_gene_list: Read genes list

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

Read genes list

Description

Function employed for reading all the gene lists on which the enrichment will be performed.

Usage

read_gene_list(
  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 assigned to the folder in which outputs are saved. Default is: "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, both up and down regulated genes (up_down_genes), only up regulated genes (up_genes), only down regulated genes (down_genes), or everything allow to load all the three kind of lists separately.
from_DE_analysis	Default is TRUE, set FALSE if the lists you want to upload are not from a differential expression analysis.where_files
where_files	(Default = NULL). When from_DE_analysis = T it is mandatory to provide a path to specify where the list of genes are.
files_format	(Default = NULL). when from_DE_analysis = T it is mandatory to provide the extension of the list of genes to upload.

isabellagrassucci/autogo_cp documentation built on April 10, 2022, 12:05 a.m.