autoGO (version 1.0.1)

read_enrich_tables: 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(
  enrich_table_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 enrichment tables, each one being a tibble object.

Arguments

enrich_table_path

Specify the full path to the folder where enrichment tables 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, 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 and it is employed also for lists not from differential analysis.

from_autoGO

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

files_format

Default is NULL, when from_autoGO = FALSE it is mandatory to provide the extension of the list of genes you want to upload.

Examples

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