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. |
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. |
Author(s)
Oliver Bembom, bembom@berkeley.edu
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 1.8.0
Index]