freqGsea: frequence table for GSEA terms

In NicolasH2/gseaCondenser: condense GSEA information

frequence table for GSEA terms

Description

frequence table for GSEA terms

Usage

freqGsea(
  pathways,
  sep = "_",
  bias = NULL,
  clean = T,
  cleanII = T,
  removeIncluding = "",
  removeThis = ""
)

Arguments

pathways	character vector. Upper or lower case makes no matter, since everything will be converted to uppercase anyway.
sep	charachter. What separates words in a set name? E.g. if terms look like "KEGG_CELL_CYCLE", you need to set sep="_"
bias	numeric vector of the same length as the pathways vector The pathways will be counted x times (x = bias). The numbers will be rounded to integers.
clean	boolean, should common words and wordcombinations including these common words be removed? These common words include e.g. "the","of", etc. but also "GO","KEGG","REACTOME" and "PID"
cleanII	boolean, should unspecific words (but not their combination with others) be removed? E.g. "cellular","activation","alpha" etc. Combinations like il_alpha will not be removed.
removeIncluding	character vector. Listed words and combinations that include them will be removed.
removeThis	character vector. Listed words will be removed, but not combinations that include them.

Value

Data.frame containing one column "word" and one column "freq", showing how many times one word (or word-combination) came up.

Examples

library(gseaCondenser)
library(wordcloud2)

myfreq <- freqGsea(names(gseaCondenser::mySetlist))
wordcloud2(myfreq)

NicolasH2/gseaCondenser documentation built on Jan. 28, 2024, 7:25 p.m.