View source: R/ontology_analysis.R
merge_n_clean | R Documentation |
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.
merge_n_clean(diff_stage_tables, cut_level = 2, pval = 0.01, sort_by = "pvalSum", modus = "GO", show_enrich_only = TRUE)
diff_stage_tables |
put in dataframes obtained by |
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. |
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.
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