simScore {cosmo} | R Documentation

## Score motif detection simulation results

### Description

This function computes sensitivity and specifity for the results returned by cosmo.

### Usage

      simScore(truth, cosmoOut, minOverlap=0.25)

### Arguments

`truth` | `align` Alignment describing the true motif occurrences.
`cosmoOut` | `cosmo` The results returned by `cosmo()`.
`minOverlap` | `numeric` A predicted motif must overlap at least this proportion of a known motif to be considered a hit.

### Details

### Value

`sens` | The proportion of true motif occurrences discovered (sensitivity).
`spec` | The proportion of true motif occurrences among the discovered sites (specificity).
`roc` | The area under the ROC curve.

### Note

### Author(s)

Oliver Bembom, bembom@berkeley.edu

### References

### See Also

`cosmo`

### Examples

    ## generate 20 sequences according to OOPS model
    ## with an expected 50
    ## motif
    data(motifPWM)
    data(transMats)
    res <- rseq(20, 100, 1.0, motifPWM, transMats,"ZOOPS")
    truth <- res$motifs
    seqs <- res$seqs

    res <- cosmo(seqs, constraints="None", minW=8, maxW=8)
    simScore(truth, res)

[Package cosmo version 1.2.0 Index]