count_word_from_GO {simplifyEnrichment} | R Documentation |
Calculate word frequency From GO
count_word_from_GO(go_id, term = NULL, exclude_words = NULL)
go_id |
A vector of GO IDs. |
term |
The corresponding names or description of terms if the input are not GO terms. |
exclude_words |
The words that should be excluded. |
The input can be simply set with a vector of GO id to go_id
argument so that the GO names
are automatically extracted. Users can also provide a vector of long names/descriptions by term
argument.
If the input is GO id, the following words are excluded: c("via", "protein", "factor", "side", "type", "specific")
.
They are analyzed by simplifyEnrichment:::all_GO_word_count()
.
A data frame with words and frequencies.
gm = readRDS(system.file("extdata", "random_GO_BP_sim_mat.rds", package = "simplifyEnrichment")) go_id = rownames(gm) head(count_word_from_GO(go_id))