binomRegMethModelPlot: Plot the smooth covariate effect

In kaiqiong/SOMNiBUS: Smooth modeling of bisulfite sequencing

Plot the smooth covariate effect

Description

This function accepts an output object from function binomRegMethModel and print out a plot of the estimated effect across the region for each test covariate.

Usage

binomRegMethModelPlot(
  BEM.obj,
  mfrow = NULL,
  same.range = FALSE,
  title = "Smooth covariate effects",
  covs = NULL,
  save = NULL,
  verbose = TRUE
)

Arguments

BEM.obj	an output object from function binomRegMethModel
mfrow	A vector of the form c(nr, nc). Subsequent figures will be drawn in an nr-by-nc array on the device.
same.range	specify whether the plots should be in the same vertical scale
title	the text for the title
covs	a vector of covariate names. The covariates with names in covs will be included in the plot. When the value is set to NULL all the covariates and the Intercept will be represented. The default value is NULL.
save	file name to create on disk. When the value is set to NULL, the plot is not saved. The default value is NULL.
verbose	logical indicates if the algorithm should provide progress report information. The default value is TRUE.

Value

This function prints out a plot of smooth covariate effects and its pointwise confidence intervals

Author(s)

Kaiqiong Zhao, Audrey Lemaçon

Examples

#------------------------------------------------------------#
data(RAdat)
head(RAdat)
RAdat.f <- na.omit(RAdat[RAdat$Total_Counts != 0, ])
out <- binomRegMethModel(
  data=RAdat.f, n.k=rep(5, 3), p0=0.003307034, p1=0.9,
  epsilon=10^(-6), epsilon.lambda=10^(-3), maxStep=200,
  Quasi = FALSE, RanEff = FALSE
)
binomRegMethModelPlot(out, same.range=FALSE)

kaiqiong/SOMNiBUS documentation built on Feb. 24, 2023, 5:38 a.m.