GSEA_Source: GSEA Source Code Functions
Description
The following functions were used and published by the Broad Institute as a part of an attempt to make Gene Set Enrichment Analysis available in R. These functions are used within the functions written in this package. They are not meant to be used by the user but are made available if they need to be used.
Usage
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A,
class.labels,
gene.labels,
nperm,
permutation.type = 0,
sigma.correction = "GeneCluster",
fraction = 1,
replace = F,
reverse.sign = F,
abs.val = F
)
GSEA.EnrichmentScore(
gene.list,
gene.set,
weighted.score.type = 1,
correl.vector = NULL
)
OLD.GSEA.EnrichmentScore(gene.list, gene.set)
GSEA.EnrichmentScore2(
gene.list,
gene.set,
weighted.score.type = 1,
correl.vector = NULL
)
GSEA.HeatMapPlot(
V,
row.names = F,
col.labels,
col.classes,
col.names = F,
main = " ",
xlab = " ",
ylab = " "
)
GSEA.Res2Frame(filename = "NULL")
GSEA.Gct2Frame(filename = "NULL")
GSEA.Gct2Frame2(filename = "NULL")
GSEA.ReadClsFile(file = "NULL")
GSEA.Threshold(V, thres, ceil)
GSEA.VarFilter(V, fold, delta, gene.names = "NULL")
GSEA.NormalizeRows(V)
GSEA.NormalizeCols(V)
GSEA(
input.ds,
input.cls,
gene.ann = "",
gs.db,
gs.ann = "",
output.directory = "",
output.directory2 = "",
doc.string = "GSEA.analysis",
non.interactive.run = F,
reshuffling.type = "sample.labels",
nperm = 1000,
weighted.score.type = 1,
nom.p.val.threshold = -1,
fwer.p.val.threshold = -1,
topgs = 10,
adjust.FDR.q.val = F,
reverse.sign = F,
preproc.type = 0,
random.seed = 123456,
perm.type = 0,
fraction = 1,
replace = F,
save.intermediate.results = F,
OLD.GSEA = F,
use.fast.enrichment.routine = T,
abs.val = F
)
|
References
Subramanian, Tamayo, et al. (2005), PNAS 102, 15545-15550, http://www.broad.mit.edu/gsea/
