In tkostas/komics: Tools to analyze omics data

You have assigned keywords for each protein in you dataset in one column. The multiple keywords are separated by and identifier (e.g. "; "). After testing your dataset for differential abundance, you plan to identify enriched keywords. Use the kwd_enrichment() function to test if a specific term of your interest is over-represended in the enriched sub-proteome over the background proteins (complete proteome). see example

# you can have the keywords in the same dataframe with your ids. 
# e.g. from a central annotation file you can used the append_cols_df function to add 
#      annotation in your working dataframe
# crete two vectors with the keywords for the significant ids and the background
kwd_col_test <- NS_secreted$Keyword
kwd_col_bg <- bg_secreted$Keyword

# crete a vector with the keywords that you aim to test
my_keywords <- c("proteolysis", "transport", "immune system")

# define the separator if multiple keywords are used for each entry
kwd_sep <- "; "

kwd_enrichment(kwd_col_test = significant_ids$keywords,
               kwd_col_bg = background_set$keywords,
               kwd_vector = my_keywords, 
               padj_method = "bonferonni")