Method | Default Parameters |
---|---|
GSEA | Data File: Inputted txt file Response File: Inputted txt file Knowledge base: mSigDB gmx file Num. Permutations: 1000 Permutation Type: Gene or Phenotype Scoring Scheme: Weighted Ranking Metric: Signal To Noise |
SAFE | Data Matrix (X.mat): Inputted rda file Response Vector (y.vec): Inputted rda file Gene Category Assignments (C.mat): Created from gmt file Method: Permutation Min Category Size: 2 Max Category Size: Inf by.gene: FALSE Local Statistic: Student T-Test (“t.Student”) Global Statistic: Wilcoxon Rank Sum (“Wilcoxon”) Args.global: list(one.sided = F) Num. of Permutations (‘Pi.mat’): 1000 Multiple Testing Correction (‘error’): FDR.BH |
sigPathway | Data File: Inputted rda file Knowledge base: mSigDB gmx file Min gene set size: 1 Max gene set size: 10,000 allPathways: TRUE Number of Pathways: length(mSigDB gmx file) |
CAMERA | Data File: Inputted rda file Response Inputted rda file Knowledge base: mSigDB gmx file |