subMotifCon-class {cosmo}R Documentation

Class "subMotifCon" ~~~

Description

This class defines a global constraint when a part of the motif is partially known.

Objects from the Class

Objects can be created by calls of the form new('subMotifCon',
submotif = ...., # Object of class \code{character}
minfreq = ...., # Object of class \code{numeric}
) or by: makeSubMotifCon(
submotif = ...., # Object of class \code{character}
minfreq = ...., # Object of class \code{numeric} indicates the lower bound for the nucleotide frequencies in order for the submotif to be considered as contained within the motif.The nucleotide frequencies are determined from the estinmated position weight matrix.
)

Slots

submotif:
Object of class "matrix", it is the submotif which is thought to be contained within the motif
minfreq:
Object of class "numeric" indicates the lower bound for the nucleotide frequencies in order for the submotif to be considered as contained within the motif. The nucleotide frequencies are determined from the estinmated position weight matrix.

Methods

No methods defined with class "shapeDiffCon" in the signature.

Note

Author(s)

Fabian Gallusser, fgallusser@berkeley.edu

References

See Also

shapeCon, shapeDiffCon, posFreqCon, boundCon, palCon makeConSet

Examples

submotifcon=makeSubMotifCon("TATAA", 0.5)

[Package cosmo version 1.4.0 Index]