autoGO (version 1.0.1)

read_gene_lists: Read all the genes lists

Description

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

Usage

read_gene_lists(
  gene_lists_path = "./results",
  log2FC_threshold = 0,
  padj_threshold = 0.05,
  which_list = c("up_genes", "down_genes", "up_down_genes", "everything"),
  from_autoGO = TRUE,
  files_format = NULL
)

Value

List of gene lists, each one being a one-dimensional data.frame.

Arguments

gene_lists_path

Specify the full path to the folder where the gene lists have to read from (all fitting files in any subdirectory will be loaded).

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

It can be: "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 and it is employed also for lists not from differential analysis..

from_autoGO

Default is TRUE, set FALSE if the gene list you want to upload are not from a differential expression analysis.

files_format

(Default = NULL). When from_autoGO = FALSE it is mandatory to provide the extension of the list of genes to upload.

Examples

if (FALSE) {
gene_lists <- read_gene_lists(
  gene_lists_path = "./results",
  log2FC_threshold = 0,
  padj_threshold = 0.05,
  which_list = "down_genes",
  from_autoGO = T,
  files_format = NULL
)
}