label_prop_gsea {gsean} | R Documentation |
ORA is performed by GSEA with the label propagation algorithm
label_prop_gsea(geneset, x, adjacency, threshold = 0.99, nperm = 1000, minSize = 1, maxSize = Inf, gseaParam = 1, nproc = 0, BPPARAM = NULL, ...)
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 |
GSEA result
Dongmin Jung
fgsea::fgsea, RANKS::label.prop
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)