Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation
Fig 3
Assessment of performance of seqArchR on simulated data.
(A) Adjusted Rand index (ARI) attained by seqArchR with various parameter combinations on simulated data (1000 sequences) (data described in Table 1). Bar heights represent average over ten runs. Experiments are performed for various chunk sizes, mutation rates (m) and number of mutated motif positions (p). (B) ARI attained by NPLB for 1000 sequences setting. (C, D) ARI attained by seqArchR and NPLB respectively for two scaled up versions of the simulated data: 5000 and 10000 sequences. See main text for more details. (E, F) Time taken by seqArchR and NPLB respectively to process simulated data (see main text for details).