gsePathway: gsePathway
In GuangchuangYu/ReactomePA: Reactome Pathway Analysis

Description Usage Arguments Value Author(s)

View source: R/gseAnalyzer.R

Gene Set Enrichment Analysis of Reactome Pathway

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gsePathway(geneList, organism = "human", exponent = 1, nPerm = 1000,
  minGSSize = 10, maxGSSize = 500, pvalueCutoff = 0.05,
  pAdjustMethod = "BH", verbose = TRUE, seed = FALSE, by = "fgsea")

`geneList`	order ranked geneList
`organism`	organism
`exponent`	weight of each step
`nPerm`	permutation numbers
`minGSSize`	minimal size of each geneSet for analyzing
`maxGSSize`	maximal size of each geneSet for analyzing
`pvalueCutoff`	pvalue Cutoff
`pAdjustMethod`	pvalue adjustment method
`verbose`	print message or not
`seed`	logical
`by`	one of 'fgsea' or 'DOSE'

gseaResult object

Yu Guangchuang

GuangchuangYu/ReactomePA documentation built on Dec. 4, 2019, 10:07 p.m.

GuangchuangYu/ReactomePA index

wBoot: Bootstrap Methods

DBI: R Database Interface

glasso: Graphical Lasso: Estimation of Gaussian Graphical Models

AMIAS: Alternating Minimization Induced Active Set Algorithms

tseriesEntropy: Entropy Based Analysis and Tests for Time Series

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