plot-Intercept-ANY-method: Plot Intercept Plots object of class Intercept with specific...

In BussemakerLab/SelexGLM: Functions for performing feature-based analyis of SELEX-seq data using generalized linear models

Description

Plot Intercept

Plots object of class Intercept with specific methods for multi-round fitting and view- and strand-specific offsets.

Usage

## S4 method for signature 'Intercept,ANY'
plot(x, sumI, includeRound, includeView,
  includeDNAstrand, rcSymmetric, title = NULL, iter = NULL)

Arguments

x	Object of class Intercept.
sumI	Intercept part of design matrix summary.
includeRound	logical: indicating whether or not plots of ddG values for different rounds should be included. If no value is indicated, Intercept object will be used to infer whether multiple rounds were fit (includeRound = TRUE) or only one round was used (includeRound = FALSE).
includeView	logical: indicating whether or not affinities for different views should be plotted. If no value is indicated, Intercept object will be used to infer whether individual views were fit (includeView = TRUE) or only one round was used (includeView = FALSE).
rcSymmetric	logical: indicating whether reverse complement symmetric version of plotting should be used. If no value is indicated, Intercept object will be used to infer whether reverse complement symmetrized values were fit (rcSymmetric = TRUE) or not (rcSymmetric = FALSE).
title	Optional title parameter to be used for plot
iter	Iteration of beta values to be used in plot. If iteration == NULL, the most recent round of beta values are used.
includeDNAStrand	logical: indicating whether or not affinities for different DNA strands should be plotted. If no value is indicated, Intercept object will be used to infer whether individual strands but not views were fit (includeDNAStrand = TRUE) or not (includeDNAStrand = FALSE).

Value

ggplot Plots of Intercept values

BussemakerLab/SelexGLM documentation built on May 17, 2019, 5:41 p.m.