Description Usage Arguments Value Author(s) See Also Examples

View source: R/gespeR-concordance.R

Measures include the correlation (rho) between pairs of phenotypes for the same gene, the rank biased overlap (`rbo`

)
of the top and bottom of ranked lists, and the Jaccard index (J) of selected genes.

1 2 | ```
concordance(..., min.overlap = 10, cor.method = "spearman", rbo.p = 0.98,
rbo.k = NULL, rbo.mid = 0, uneven.lengths = TRUE)
``` |

`...` |
The phenotypes to be evaluated for concordance |

`min.overlap` |
The minimum number of overlapping genes required |

`cor.method` |
A character string indicating which correlation coefficient is to be computed |

`rbo.p` |
The weighting parameter for rank biased overlap (rbo) in [0, 1]. High p implies strong emphasis on top ranked elements |

`rbo.k` |
The evaluation depth for rank biased overlap extrapolation |

`rbo.mid` |
The mid point to split a ranked list, e.g. in order to split positive and negative scores choose mid=0 |

`uneven.lengths` |
Indicator if lists have uneven lengths |

A `concordance`

object with the following elements:

`pair.test` |
Indicator of compared phenotypes |

`cor` |
The correlation between pairs of phenotypes for the same gene |

`rbo.top` |
The rank biased overlap of genes evaluated at the top of the ranked list |

`rbo.bottom` |
The rank biased overlap of genes evaluated at the bottom of the ranked list |

`jaccard` |
The Jaccard index of selected genes |

Fabian Schmich

1 2 3 4 | ```
data(stabilityfits)
conc <- concordance(gsp(stabilityfits$A), gsp(stabilityfits$B),
gsp(stabilityfits$C), gsp(stabilityfits$D))
plot(conc)
``` |

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