clear: Clear

In cashoes/sear: Simple (effin') enrichment analysis in R

Clear

Description

Clear

Usage

clear(leading_edge, cutoff = 0.25, trim = FALSE)

Arguments

leading_edge	The output of running sear on an input list of mRNAs or miRNA symbols.
cutoff	A numeric value between 0 and 1. The minimum value of the jaccard coefficient to show links between genesets.
trim	A logical value. Whether to perform trimming of non-connected nodes.

Examples

library(dplyr)
data('collections')
input <- collections$members_mrna %>% unlist() %>% unique() %>% sample(100)
output <- sear(input, type = 'mrna', return_members = TRUE) %>%
  dplyr::arrange(fdr) %>%
  dplyr::slice(1:100)
clear(output, cutoff = 0.25, trim = TRUE)

cashoes/sear documentation built on Feb. 16, 2024, 6:45 a.m.