GSEA.java.exec: Title
In jhart99/gseasier: Run the GSEA java pacakage from inside R

Title

GSEA.java.exec(input.ds, input.cls, gs.db, output.directory = "",
  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 = 20,
  adjust.FDR.q.val = F, gs.size.threshold.min = 15,
  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, metric = "Signal2Noise", contrast = "",
  silent = T)

`input.ds`	Input gene expression Affy dataset file in RES or GCT format
`input.cls`	Input class vector (phenotype) file in CLS format
`gs.db`	Gene set database in GMT format
`output.directory`	Directory where to store output and results (default: "")
`doc.string`	Documentation string used as a prefix to name result files (default: "GSEA.analysis")
`non.interactive.run`	Run in interactive (i.e. R GUI) or batch (R command line) mode (default: F)
`reshuffling.type`	Type of permutation reshuffling: "sample.labels" or "gene.labels" (default: "sample.labels"
`nperm`	Number of random permutations (default: 1000)
`weighted.score.type`	Enrichment correlation-based weighting: 0=no weight (KS), 1= weigthed, 2 = over-weigthed (default: 1)
`nom.p.val.threshold`	Significance threshold for nominal p-vals for gene sets (default: -1, no thres)
`fwer.p.val.threshold`	Significance threshold for FWER p-vals for gene sets (default: -1, no thres)
`fdr.q.val.threshold`	Significance threshold for FDR q-vals for gene sets (default: 0.25)
`topgs`	Besides those passing test, number of top scoring gene sets used for detailed reports (default: 10)
`adjust.FDR.q.val`	Adjust the FDR q-vals (default: F)
`gs.size.threshold.min`	Minimum size (in genes) for database gene sets to be considered (default: 25)
`gs.size.threshold.max`	Maximum size (in genes) for database gene sets to be considered (default: 500)
`reverse.sign`	Reverse direction of gene list (pos. enrichment becomes negative, etc.) (default: F)
`preproc.type`	Preproc.normalization: 0=none, 1=col(z-score)., 2=col(rank) and row(z-score)., 3=col(rank). (def: 0)
`random.seed`	Random number generator seed. (default: 123456)
`perm.type`	For experts only. Permutation type: 0 = unbalanced, 1 = balanced (default: 0)
`fraction`	For experts only. Subsampling fraction. Set to 1.0 (no resampling) (default: 1.0)
`replace`	For experts only, Resampling mode (replacement or not replacement) (default: F)
`save.intermediate.results`	For experts only, save intermediate results (e.g. matrix of random perm. scores) (default: F)
`OLD.GSEA`	Use original (old) version of GSEA (default: F)
`use.fast.enrichment.routine`	Use faster routine to compute enrichment for random permutations (default: T)
`silent`