merge_n_clean: Merge the dataframes of different stages and cut out general...

View source: R/ontology_analysis.R

merge_n_cleanR Documentation

Merge the dataframes of different stages and cut out general GO terms

Description

merge_n_clean() takes the the data output of term_enrichment() for different stages, merges them, cuts out more general GO terms and subsets the merged tables by the GO terms that are significantly enriched or depleted in any of the entered stages.

Usage

merge_n_clean(diff_stage_tables, cut_level = 2, pval = 0.01,
  sort_by = "pvalSum", modus = "GO", show_enrich_only = TRUE)

Arguments

diff_stage_tables

put in dataframes obtained by term_enrichment for several stages as list

cut_level

up to which level starting from the root the terms should be deleted ? Defaults to 2.

sort_by

how should the terms be sorted for the ggplot script ? The default is "pvalSum" and it sorts the terms according to the sum of p-values over the different stages. The second option is "variance" which sorts the terms according to the biggest spread in p-values over the stages.

modus

"GO", "PANTHER" or "KEGG"

show_enrich_only

If set to TRUE, TERMs that are depleted over all stages are ingnored for the output. Defaults to TRUE.

Value

The output is a list of two items.
The first item identified by "table_all_stages_sign_IDs" is a dataframe which contains all Ontology IDs that are significantly enriched or depleted in any of the experimental stages. This dataframe is the input for the ggplot script
The second item identified by "order_by_pval" specifies the order of terms for the visualization in the ggplot script.


zellerino/BOAT---biological-ontology-analysis-tool documentation built on Jan. 27, 2023, 3:38 p.m.