align-class {cosmo} | R Documentation |
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 can be created by calls of the form new("align", ...)
.
seq
:"numeric"
The sequences on
which the sites were predicted.pos
:"numeric"
The starting
postions of the discovered sites. orient
:"numeric"
The orientation in
which each motif was discovered: 1 for the forward strand
orientation, and -1 for the reverse complement orientationmotif
:"character"
The site
that was predicted to be a motif occurrence. prob
:"numeric"
The posterior
probability of a motif occurrence at this position eval
:"numeric"
The E-value of
the multiple alignment containing the predicted motif occurrences
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.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. 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. Oliver Bembom, bembom@berkeley.edu