centrality_gsea: Gene Set Enrichment Analysis with centrality measure
In gsean: Gene Set Enrichment Analysis with Networks

Description Usage Arguments Value Author(s) See Also Examples

View source: R/centrality_gsea.R

GSEA is performed with centrality measure

centrality_gsea(geneset, x, adjacency, pseudo = 1, nperm = 1000,
                centrality = function(x) rowSums(abs(x)),
                weightParam = 1, minSize = 1, maxSize = Inf,
                gseaParam = 1, nproc = 0, BPPARAM = NULL)

`geneset`	list of gene sets
`x`	Named vector of gene-level statistics. Names should be the same as in gene sets.
`adjacency`	adjacency matrix
`pseudo`	pseudo number for log2 transformation (default: 1)
`nperm`	number of permutations (default: 1000)
`centrality`	centrality measure, degree centrality or node strength is default
`weightParam`	weight parameter value for the centrality measure, equally weight if weightParam = 0 (default: 1)
`minSize`	minimal size of a gene set (default: 1)
`maxSize`	maximal size of a gene set (default: Inf)
`gseaParam`	GSEA parameter value (default: 1)
`nproc`	see fgsea::fgsea
`BPPARAM`	see fgsea::fgsea

GSEA result

Dongmin Jung

fgsea::fgsea

data(examplePathways)
data(exampleRanks)
exampleRanks <- exampleRanks[1:100]
adjacency <- diag(length(exampleRanks))
rownames(adjacency) <- names(exampleRanks)
set.seed(1)
result.GSEA <- centrality_gsea(examplePathways, exampleRanks, adjacency)

Loading required package: fgsea
Loading required package: PPInfer
Loading required package: biomaRt
Loading required package: kernlab
Loading required package: ggplot2

Attaching package: ‘ggplot2’

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Loading required package: igraph

Attaching package: ‘igraph’

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Loading required package: STRINGdb
Loading required package: yeastExpData
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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Attaching package: ‘graph’

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sh: 1: wc: Permission denied
Warning message:
In fgsea(geneset, statistic, nperm = nperm, minSize = minSize, maxSize = maxSize,  :
  You are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument in the fgsea function call.