makePosFreqCon {cosmo}R Documentation

Constructing a nucleotide frequency constraint

Description

This function constructs a texttt{posFreqCon} object representing a constraint on the unknown position weight matrix that requires the frequency of a given nucleotide to be above a given lower bound, either at a single position in a given interval, or on average across the entire interval

Usage

makePosFreqCon(pos, nuc, lower)

Arguments

pos This is either the string avg, indicating that the average nucleotide frequency across the interval is bounded from below, or a position in the interval, indicating the nucleotide frequency at that position in the interval is bounded from below.
nuc character This is one of A, C, G, T, GC, AT.
lower numeric the lower bound on the nucleotide frequency of interest

Value

An object of class texttt{posFreqCon}.

Author(s)

Fabian Gallusser, fgallusser@berkeley.edu

See Also

boundCon, shapeCon, subMotifCon, posFreqCon, shapeDiffCon, palCon

Examples

pfc <- makePosFreqCon("avg","GC", 0.75)

[Package cosmo version 1.8.0 Index]