simplify {clusterProfiler}R Documentation

simplify method

Description

simplify output from enrichGO and 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

Value

updated enrichResult object

updated compareClusterResult object

Author(s)

Guangchuang Yu

Gwang-Jin Kim and Guangchuang Yu

Guangchuang Yu

References

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

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


[Package clusterProfiler version 4.2.1 Index]