GSEA_Source: GSEA Source Code Functions

In kelsiereinaltt/GSEApackage: GSEA Analysis and Plotting Function

Description

These functions were written by the Broad Institute and published as a part of their attempt to make their Gene Set Enrichment Analysis able to be run 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

GSEA.GeneRanking(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, fdr.q.val.threshold = 0.25, topgs = 10,
  adjust.FDR.q.val = F, gs.size.threshold.min = 25,
  gs.size.threshold.max = 500, 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/

kelsiereinaltt/GSEApackage documentation built on May 27, 2020, 12:05 a.m.