BCRANKsearch-class: Class "BCRANKsearch"
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 objectObjects 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.