Description Usage Arguments Examples
View source: R/kwd_enrichment.R
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.
1 2 | kwd_enrichment(kwd_col_test, kwd_col_bg, kwd_vector, kwd_sep = "; ",
padj_method = "bonferroni")
|
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 |
kwd_col_bg |
Similar with the |
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. |
1 2 3 | kwd_enrichment(kwd_col_test = significant_ids$keywords,
kwd_col_bg = background_set$keywords,
kwd_vector = c("proteolysis", "transport", "immune system"))
|
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