kwd_enrichment: Test for keyword enrichment in the differentially...

Description Usage Arguments Examples

View source: R/kwd_enrichment.R

Description

Reads a list of keywords and tests for enrichment in a subset of genes/proteins over the background. As background can be selected the total list of ids or the complete genome/proteome. Significant enrichment is tested using Fisher's exact test. Calculated p-values are furhter adjusted for multiple hypothesis testing error. See arguments for more info.

Usage

1
2
kwd_enrichment(kwd_col_test, kwd_col_bg, kwd_vector, kwd_sep = "; ",
  padj_method = "bonferroni")

Arguments

kwd_col_test

A vector containing keywords for the differentially abundant/expressed ids. Multiple keywords can be included for each cell, separated by and identifier (by default '; '). Each element of the vector can contain keywords for a specific protein. You can add filter your dataset to the ids of interest, add annotation using append_cols_df() function, and add assign the corresponding column (e.g. kwd_col_test = my_data$keywords).

kwd_col_bg

Similar with the kwd_col_test, is a vector containing keywords for the ids of background genome/proteome.

kwd_vector

A character vector containing the keywords that you want to test for significance. Each keyword will be matched exactly, but there is an elasticity for the use of upper or lower case characters.

kwd_sep

In case that multiple keywords are provided for each protein/gene, you can choose the keyword seperator. Default value is "; ".

padj_method

Keywords will be tested for significance using Fisher's exact test. P-values will be further adjusted, by default using "bonverroni" method. See \?p.adjust() for more info.

Examples

1
2
3
kwd_enrichment(kwd_col_test = significant_ids$keywords,
               kwd_col_bg = background_set$keywords,
               kwd_vector = c("proteolysis", "transport", "immune system"))

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