runEA | R Documentation |
This function applies selected methods for enrichment analysis to selected datasets of a compendium.
runEA(
exp.list,
methods,
gs,
perm = 1000,
parallel = NULL,
save2file = FALSE,
out.dir = NULL,
...
)
exp.list |
Experiment list. A |
methods |
Methods for enrichment analysis. This can be either
|
gs |
Gene sets, i.e. a list of character vectors of gene IDs. |
perm |
Number of permutations of the sample group assignments.
Defaults to 1000. Can also be an integer vector matching
the length of |
parallel |
Parallel computation mode. An instance of class
|
save2file |
Logical. Should results be saved to file for subsequent
benchmarking? Defaults to |
out.dir |
Character. Determines the output directory where results are
saved to. Defaults to |
... |
Additional arguments passed to the selected enrichment methods. |
A list with an entry for each method applied. Each method entry is a list with an entry for each dataset analyzed. Each dataset entry is a list of length 2, with the first element being the runtime and the second element being the gene set ranking, as obtained from applying the respective method to the respective dataset.
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
sbea
and nbea
for carrying out set- and network-based enrichment analysis.
BiocParallelParam
and register
for
configuration of parallel computation.
# loading three datasets from the GEO2KEGG compendium
geo2kegg <- loadEData("geo2kegg", nr.datasets=3)
# only considering the first 1000 probes for demonstration
geo2kegg <- lapply(geo2kegg, function(d) d[1:1000,])
# preprocessing and DE analysis for two of the datasets
geo2kegg <- maPreproc(geo2kegg[2:3])
geo2kegg <- runDE(geo2kegg)
# getting a subset of human KEGG gene sets
gs.file <- system.file("extdata/hsa_kegg_gs.gmt", package="EnrichmentBrowser")
kegg.gs <- EnrichmentBrowser::getGenesets(gs.file)
# applying two methods to two datasets
res <- runEA(geo2kegg, methods=c("ora", "camera"), gs=kegg.gs, perm=0)
# applying a user-defined enrichment method
dummySBEA <- function(se, gs)
{
sig.ps <- sample(seq(0, 0.05, length=1000), 5)
nsig.ps <- sample(seq(0.1, 1, length=1000), length(gs)-5)
ps <- sample(c(sig.ps, nsig.ps), length(gs))
names(ps) <- names(gs)
return(ps)
}
res <- runEA(geo2kegg, methods=dummySBEA, gs=kegg.gs)
# applying a mix of pre-defined and user-defined methods
methods <- list(camera = "camera", dummySBEA = dummySBEA)
res <- runEA(geo2kegg, methods, gs=kegg.gs, perm=0)
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