simplify {clusterProfiler}R Documentation

simplify method

Description

simplify output from enrichGO by removing redundancy of enriched GO terms

simplify output from gseGO by removing redundancy of enriched GO terms

simplify output from compareCluster by removing redundancy of enriched GO terms

Usage

## S4 method for signature 'enrichResult'
simplify(x, cutoff = 0.7, by = "p.adjust",
  select_fun = min, measure = "Wang", semData = NULL)

## S4 method for signature 'gseaResult'
simplify(x, cutoff = 0.7, by = "p.adjust",
  select_fun = min, measure = "Wang", semData = NULL)

## S4 method for signature 'compareClusterResult'
simplify(x, cutoff = 0.7,
  by = "p.adjust", select_fun = min, measure = "Wang",
  semData = NULL)

Arguments

x

output of enrichGO

cutoff

similarity cutoff

by

feature to select representative term, selected by 'select_fun' function

select_fun

function to select feature passed by 'by' parameter

measure

method to measure similarity

semData

GOSemSimDATA object

x

output of gseGO

cutoff

similarity cutoff

by

feature to select representative term, selected by 'select_fun' function

select_fun

function to select feature passed by 'by' parameter

measure

method to measure similarity

semData

GOSemSimDATA object

Value

updated enrichResult object

updated gseaResult object

updated compareClusterResult object

Author(s)

Guangchuang Yu

Gwang-Jin Kim

Guangchuang Yu

References

issue #28 https://github.com/GuangchuangYu/clusterProfiler/issues/28

issue #162 https://github.com/GuangchuangYu/clusterProfiler/issues/162


[Package clusterProfiler version 3.10.1 Index]