concordance {gespeR} | R Documentation

## Evaluate the concordance between Phenotype objects

### Description

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.

### Usage

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

### Arguments

`...` | 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

### Value

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

### Author(s)

Fabian Schmich

### See Also

`Phenotypes`

`plot.concordance`

`rbo`

### Examples

    data(stabilityfits)
    conc <- concordance(gsp(stabilityfits$A), gsp(stabilityfits$B),
    gsp(stabilityfits$C), gsp(stabilityfits$D))
    plot(conc)

[Package gespeR version 1.18.0 Index]