Description Usage Arguments Details Value Author(s) References Examples

Ranks are used to score genes with respect to degree of agreement to a given trend or pattern, Lehmann (1974) p.294.

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`data` |
A data frame with one array in each column |

`pattern` |
A permutation of the integers 1:ncol(data) |

`har` |
logical parameter indicating whether or not a score based on Hardy's theorem shall be calculated. |

The rank scores gives a higher weight to a deviation from trend in more distant obseveations than a deviation between neighbouring observations. The p-values are calculated through a normal approximation.

A list with the components

`score` |
the rank score for each gene |

`hardy` |
if har = TRUE the hardy score, NULL otherwise |

`pvals` |
the p-values for the null hypothesis of no trend |

Per Broberg

Lehmann, E.L. (1975) Nonparametrics: Statistical Methods Based on Ranks, Holden-Day

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