BCRANKsearch-class: Class "BCRANKsearch"


Holds the whole search path from a single bcrank run. Each individual search step is stored in a BCRANKmatch-class object. Several objects of this class are collected in a BCRANKresult-class object

Objects from the Class

Objects are not intended to be created directly but as a result from running bcrank.



a collection of BCRANKmatch-class objects, ontaining all bcrank search steps from a start guess to a locally optimal solution.


a BCRANKmatch-class object 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 i is NULL, returns a data frame containing consensus and score for the whole search path. Otherwise, the i'th BCRANKmatch-class object 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 normalize is TRUE. When FALSE, the number of matching sequences is reported.


signature(x = "BCRANKsearch", y = "missing"): A plot method for the searchPath.


Adam Ameur, adam.ameur@genpat.uu.se

See Also

bcrank, BCRANKmatch-class, BCRANKresult-class

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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