PerformMetaPSEA: PerformMetaPSEA Function to perform peak set enrichment...

In xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data

PerformMetaPSEA Function to perform peak set enrichment meta-analysis at either the empirical compound, compound level or pathway level.

Description

This is the main function that performs either the mummichog algorithm, GSEA, or both for peak set enrichment meta-analysis.

Usage

PerformMetaPSEA(
  mSetObj = NA,
  lib,
  libVersion,
  minLib = 3,
  permNum = 100,
  metaLevel = "pathway",
  combine.level = "pvalue",
  pval.method = "fisher",
  es.method = "fixed",
  rank.metric = "mean",
  mutual.feats = TRUE,
  pooled_cutoff = 0.05
)

Arguments

mSetObj	Input the name of the created mSetObj object.
lib	Input the name of the organism library, default is hsa_mfn.
libVersion	Input the version of the KEGG pathway libraries ("current" or "old").
minLib	numeric, default is 3
permNum	Numeric, input the number of permutations to perform. Default is 100.
metaLevel	Character, input whether the meta-analysis is at the empirical compound ("ec"), compound ("cpd"), or pathway level ("pathway").
combine.level	Character, input whether to combine p-values or pool the peaks.
pval.method	Character, input the method to perform p-value combination.
es.method	Character, input the method to perform effect-size meta-analysis.
rank.metric	Character, input how to calculate pre-ranking metric. "mean" to use the average, "min" to use the lowest score, "max" to use the highest score.
mutual.feats	mutual.feats, logical
pooled_cutoff	pooled_cutoff, numeric

Author(s)

Jasmine Chong, Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MetaboAnalystR documentation built on Dec. 23, 2024, 3:44 p.m.