kwd_enrichment_multi: Keyword enrichment for multiple categories

Description Usage Arguments Examples

View source: R/kwd_enrichment_multi.R

Description

Reads multiple category identifiers and performes a keyword enrichment for each combination of test/background group (see kwd_enrichment). The output is a list of tables.

Usage

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kwd_enrichment_multi(x, categories, test_keywords, grouping_col,
  keywords_col = "keywords", padj_method = "BH")

Arguments

x

A dataframe with the values.

categories

A character vector containing the categories that will be tested.

test_keywords

A caracter vector with the keywords to be tested.

grouping_col

A character string matching exactly the column of the dataframe x that contains the labaled for each category.

keywords_col

A character string matching exactly the column of the dataframe x that contains the keywords.

padj_method

Method to adjust the p-values of the enrichment test (Fisher exact test). See link{p.adjust} for more info.

Examples

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  test_keywords <- c("protease",
                     "solute binding protein",
                     "oxidoreductase",
                     "transport",
                     "virulence")

  categories <- c("stable", "decreasing", "increasing")
  category_comparison <- kwd_enrichment_multi(x = merged_data,
                                              categories = categories,
                                              grouping_col = "Grouping_col",
                                              test_keywords = test_keywords)

tkostas/komics documentation built on May 24, 2019, 7:31 a.m.