cfm: Confusion Matrix

In MyersGroup/MotifFinder: A Bayesian, De Novo, Joint Motif Finder

Description

Confusion Matrix

Usage

cfm(motif_found, simulated_sequences, complement = F)

Arguments

simulated_sequences	list; Output of simulate_sequences
complement	logical; Did findamotif return the complemented version of the simulated motif Change this if you get 0 true positives
found_motif	list; The output of getmotifs() or findamotif()

Details

Note that for a positive match, all of the sequence, strand and position of the motif. A mismatch in any of these will exclude a predicted +ve true +ve. However the total number of true -ve does not count each position as one negative but each sequence which does not contain an added motif.

Also note that there could be matches to your simulated motif by chance in random sequence, and as the motif generation is probabilistic, some sequences with the motif added will not be a good match to the consensus motif.

Value

List of confusion matricies, one for overall and one each for each strand

MyersGroup/MotifFinder documentation built on June 7, 2019, 3:42 p.m.