Description Usage Arguments Examples
Gene set enrichment analysis
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values |
vector of values with associated gene names; values must be named, according to names appearing in set elements |
geneset |
vector of genes in the gene set |
power |
an exponent to control the weight of the step (default: 1) |
rank |
whether to use ranks as opposed to values (default: FALSE) |
weight |
additional weights associated with each value (default: rep(1,length(values))) |
n.rand |
number of random permutations used to assess significance (default: 1e4) |
plot |
whether to plot (default: TRUE) |
main |
plot title (default: "") |
return.details |
whether to return extended details (default: FALSE) |
quantile.threshold |
threshold used (default: min(100/n.rand,0.1)) |
random.seed |
random seed (default: 1) |
mc.cores |
number of cores for parallel processing (default: 1) |
1 2 3 4 5 6 7 8 9 | data("org.Hs.GO2Symbol.list")
universe <- unique(unlist(org.Hs.GO2Symbol.list)) # get universe
gs <- org.Hs.GO2Symbol.list[[1]] # get a gene set
# fake dummy example where everything in gene set is perfectly enriched
vals <- rnorm(length(universe), 0, 10)
names(vals) <- universe
vals[gs] <- rnorm(length(gs), 100, 10)
# test obviously enriched set, reduce n.rand for speed
gsea(values=vals, geneset=gs, mc.cores=1, n.rand=100, main="GO:Random")
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