postProbs-class {cosmo}R Documentation

Class "postProbs"

Description

An object of class "postProbs" collects information about the posterior probability of motif occurrences in each of the eligible positions of the input sequences. Most notably these probabilities can be plotted using the plot function.

Objects from the Class

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

Slots

seqMat:
Object of class "matrix" The sequences in numerical matrix format as output by cosmo.
seqNames:
"list"A list of the sequence names.
probs:
"numeric"A matrix of the posterior probabilities.
revcomp:
"logical"A matrix indicating whether the motif is more likely to occure in the reverse complement orientation.

Methods

plot
signature(x = "postProbs") Plots the posterior probabilities. If the motif is more likely to occur in the forward strand orientation, the bar extends upward from the horizontal, otherwise it extends downward.

Author(s)

Oliver Bembom, bembom@berkeley.edu


[Package cosmo version 1.8.0 Index]