cosmo-class {cosmo} | R Documentation

## Class "cosmo"

### Description

An object of class `"cosmo"` is automatically created after calling the 'cosmo' function and summarizes the results.

### Objects from the Class

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

### Slots

`seqs`:
  A list of the input sequences.
`pwm`:
  An object of class `pwm` representing the estimated position weight matrix.
`back`:
  A data frame summarizing the candidate Markov models for the background distribution.
`tmat`:
  The estimated transition matrix/matrices used to model the distribution of background nucleotides.
`cand`:
  A data frame summarizing the candidate models considered.
`cons`:
  The constraint set applied in the final model.
`sel`:
  The selected model.
`motifs`:
  An object of class `"align"` representing the predicted motif occurrences.
`probs`:
  A list giving the posterior probabilities of motif occurrences along each sequence.
`objectCall`:
  The call which produced this object.

### Methods

summary
  `signature(object = "cosmo",...)` Summarizes the cosmo object.
plot
  `signature(x = "cosmo",type="PWM", ...)` If `type == "PWM"`, plots the sequence logo of the discovered motif. If `type == "prob"`, plots the posterior probabilities of motif occurrences along all input sequences.
print
  `signature(x = "cosmo",...)` 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 estimates position weight matrix.
show
  `signature(object = "cosmo")` 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 1.6.0 Index]