read_enrich_tables {autoGO} | R Documentation |
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
)
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. |
Value
List of enrichment tables, each one being a tibble object.
Examples
## Not run:
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
)
## End(Not run)