Holds the whole search path from a single
bcrank run. Each individual search step
is stored in a
object. Several objects of this class are collected in a
Objects from the Class
Objects are not intended to be created directly but as a result from
a collection of
BCRANKmatch-classobjects, ontaining all bcrank search steps from a start guess to a locally optimal solution.
BCRANKmatch-classobject for the highest scoring consensus sequence (locally optimal solution) in this bcrank run.
position weight matrix for the highest scoring consensus sequence.
number of occurrences of the final consensus sequence in the fasta input file.
number of iterations required to move from the start guess to the final soloution in this bcrank run.
signature(object = "BCRANKsearch", i=NULL): If
iis NULL, returns a data frame containing consensus and score for the whole search path. Otherwise, the i'th
BCRANKmatch-classobject in the search path is returned.
signature(object = "BCRANKsearch", normalize=TRUE): Returns the position weight matrix (pwm) for the highest scoring consensus in this bcrank run. Matrix positions are between between 0 and 1 when
normalizeis TRUE. When FALSE, the number of matching sequences is reported.
signature(x = "BCRANKsearch", y = "missing"): A plot method for the searchPath.
Adam Ameur, email@example.com
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