label_prop_gsea {gsean}R Documentation

Over-representaion analysis with the label propagation algorithm

Description

ORA is performed by GSEA with the label propagation algorithm

Usage

label_prop_gsea(geneset, x, adjacency, threshold = 0.99, nperm = 1000,
                minSize = 1, maxSize = Inf, gseaParam = 1, nproc = 0,
                BPPARAM = NULL, ...)

Arguments

geneset

list of gene sets

x

set of genes

adjacency

adjacency matrix

threshold

threshold of correlation for nodes to be considered neighbors (default: 0.99)

nperm

number of permutations (default: 1000)

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

...

additional parameters for label propagation; see RANKS::label.prop

Value

GSEA result

Author(s)

Dongmin Jung

See Also

fgsea::fgsea, RANKS::label.prop

Examples

data(examplePathways)
data(exampleRanks)
exampleRanks <- exampleRanks[1:100]
geneNames <- names(exampleRanks)
set.seed(1)
x <- sample(geneNames, 10)
adjacency <- diag(length(exampleRanks))
rownames(adjacency) <- geneNames
result.GSEA <- label_prop_gsea(examplePathways, x, adjacency)

[Package gsean version 1.0.0 Index]