align-class {cosmo}R Documentation

Class "align"

Description

An object of class "align" summarizes the motif occurrences that were predicted by cosmo. For each predicted motif occurrence, it contains the sequences on which the site was found, the position on that sequence, the orientation of the motif (1 if found on the forward strand, -1 otherwise), the site itself, as well as the posterior probability of a motif occurrence at that site.

Objects from the Class

Objects can be created by calls of the form new("align", ...).

Slots

seq:
Object of class "numeric" The sequences on which the sites were predicted.
pos:
Object of class "numeric" The starting postions of the discovered sites.
orient:
Object of class "numeric" The orientation in which each motif was discovered: 1 for the forward strand orientation, and -1 for the reverse complement orientation
motif:
Object of class "character" The site that was predicted to be a motif occurrence.
prob:
Object of class "numeric" The posterior probability of a motif occurrence at this position
eval:
Object of class "numeric" The E-value of the multiple alignment containing the predicted motif occurrences

Methods

summary
signature(object = "align",...) Prints the discovered motifs along with the sequences they were discovered on, the starting positions, the strand, and the posterior probability of a motif occurrence at this site. Also prints the E-value of the discovered alignment.
print
signature(x = "align",...) Prints the discovered motifs along with the sequences they were discovered on, the starting positions, the strand, and the posterior probability of a motif occurrence at this site.
show
signature(object = "align") Prints the discovered motifs along with the sequences they were discovered on, the starting positions, the strand, and the posterior probability of a motif occurrence at this site.

Note

Author(s)

Oliver Bembom, bembom@berkeley.edu

References

See Also

Examples






[Package cosmo version 1.4.0 Index]