Description Usage Arguments Value See Also Examples

This function returns a data frame of p-values, odds ratios, lower and upper confidence limits for every row of a matrix. The discovery odds ratio is calculated as using Fisher's exact test on actual counts. The test's hypothesis is whether or not the discovery of counts for a feature (of all counts) is found in greater proportion in a particular group.

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`obj` |
A MRexperiment object with a count matrix, or a simple count matrix. |

`cl` |
Group comparison |

`norm` |
Whether or not to normalize the counts - if MRexperiment object. |

`log` |
Whether or not to log2 transform the counts - if MRexperiment object. |

`adjust.method` |
Method to adjust p-values by. Default is "FDR". Options
include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr",
"none". See |

`cores` |
Number of cores to use. |

`...` |
Extra options for makeCluster |

Matrix of odds ratios, p-values, lower and upper confidence intervals

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