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.

Note

Author(s)

Oliver Bembom, bembom@berkeley.edu

References

See Also

Examples






[Package cosmo version 1.4.0 Index]