# Gene Set Benchmark

## Documentation for package ‘GSBenchMark’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

GSBenchMark-package | A list of pathways and 11 datasets consisting gene expressions and phenotypes as the benchmark for Gene Set Analysis. Most of this information was used to validate Differential Rank Conservation (DIRAC) in the first place. In addition the data in the Eddy et al. (2010) paper, we also provide two datasets.
bipolar_GDS2190 | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Bipolar
breast_GDS807 | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Breast cancer
diracpathways | The pathways downloaded from DIRAC paper
exprsdata | Gene expression matrix from DIRAC paper
GSBenchMark | A list of pathways and 11 datasets consisting gene expressions and phenotypes as the benchmark for Gene Set Analysis. Most of this information was used to validate Differential Rank Conservation (DIRAC) in the first place. In addition the data in the Eddy et al. (2010) paper, we also provide two datasets.
GSBenchMark.Dataset.names | The names of the datasets of gene expressions and phenotypes downloaded from DIRAC paper
GSBenchMarkDatasets | The names of the datasets of gene expressions and phenotypes downloaded from DIRAC paper
leukemia_GSEA | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Leukaemia
logexprsdata | Gene expression matrix from DIRAC paper
marfan_GDS2960 | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Marfan
melanoma_GDS2735 | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Melanoma
parkinsons_GDS2519 | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Parkinson's
phenotypes | A factor for binary phenotypes from DIRAC paper
phenotypesLevels | A factor for binary phenotypes from DIRAC paper
prostate_GDS2545_m_nf | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Prostate
prostate_GDS2545_m_p | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Prostate
prostate_GDS2545_p_nf | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Prostate
sarcoma_data | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Sarcoma
squamous_GDS2520 | Gene expression matrix and a factor for binary phenotypes from DIRAC paper: Squamous (Head and Neck Cancer)