Added return_all parameter to regress_pwm (multi-kmer path). When TRUE, returns every candidate-kmer regression (sorted by validation score) instead of just the best one - useful for getting N independent motifs without the residual-rounds approach used by motif_num > 1. When sample_for_kmers = TRUE, each candidate is refit on the full data.
Improved docs for regress_pwm (clarified the three operating modes, fixed n_motifs/comb_modle typos in the return-value section).
prego 0.0.9
Fix: Floating point discrepancies between predict and regress_pwm output.
prego 0.0.8
Fix: compute_local_pwm now returns NA when sequence length < motif length (issue #35).
prego 0.0.7
Fix: regress_multiple_motifs now works with multiple response variables.
prego 0.0.6
Added screen_local_pwm to find positions in sequences that match a PSSM.
Added return_list parameter to compute_local_pwm.
prego 0.0.5
Faster pssm correlation computation using RcppParallel.
pssm_match when best=FALSE now returns a score field instead of cor.
Implemented computation of KL divergence between two PSSMs. Note that spearman correlation is still the best way to match PSSMs.
prego 0.0.4
Added size paramter to intervals_to_seq.
prego 0.0.3
Added MotifDB object to store motif information.
Implmented a faster energy computation method, which is now used by default.
prego 0.0.0.9000
Added a NEWS.md file to track changes to the package.