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simplify-methods

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

clusterProfiler

statistical analysis and visualization of functional profiles for genes and gene clusters

v3.18.1
Artistic-2.0
Authors
Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Li-Gen Wang [ctb], Giovanni Dall'Olio [ctb] (formula interface of compareCluster)
Initial release

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