Class "BCRANKsearch"

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Description

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.

Slots

searchPath:

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

final:

a BCRANKmatch-class object for the highest scoring consensus sequence (locally optimal solution) in this bcrank run.

finalPWM:

position weight matrix for the highest scoring consensus sequence.

finalNrMatch:

number of occurrences of the final consensus sequence in the fasta input file.

nrIterations:

number of iterations required to move from the start guess to the final soloution in this bcrank run.

Methods

searchPath

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.

pwm

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.

plot

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

Author(s)

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

See Also

bcrank, BCRANKmatch-class, BCRANKresult-class