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.

### Author(s)

Oliver Bembom, bembom@berkeley.edu

[Package cosmo version 1.8.0 Index]