densityPlots: Draw estimated density plots for all arrays

Description Usage Arguments Value Author(s) Examples

View source: R/plotFuncs.R

Description

Draw estimated density plots for all arrays.

Usage

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densityPlots(
  es, 
  requireLog2 = TRUE, 
  myxlab = "expression level", 
  mymain = "density plots", 
  datExtrFunc = exprs, 
  fileFlag = FALSE, 
  fileFormat = "ps", 
  fileName = "densityPlots.ps")

Arguments

es

An ExpressionSet object that used to run the whole genome-wide tests.

requireLog2

logic. indicating if log2 transformation is required before estimating densities.

myxlab

character. indicating x-axis label.

mymain

character. indicating title of the plot.

datExtrFunc

name of the function to extract genomic data. For an ExpressionSet object, you should set datExtrFunc=exprs; for a MethyLumiSet object, you should set datExtrFunc=betas.

fileFlag

logic. indicating if plot should be saved to an external figure file.

fileFormat

character. indicating the figure file type. Possible values are “ps”, “pdf”, or “jpeg”. All other values will produce “png” file.

fileName

character. indicating figure file name (file extension should be specified). For example, you set fileFormat="pdf", then you can set fileName="test.pdf", but not fileName="test".

Value

A list object, the i-th element is the object returned by function density for the i-th array.

Author(s)

Weiliang Qiu <[email protected]>, Brandon Guo <[email protected]>, Christopher Anderson <[email protected]>, Barbara Klanderman <[email protected]>, Vincent Carey <[email protected]>, Benjamin Raby <[email protected]>

Examples

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  # generate simulated data set from conditional normal distribution
  set.seed(1234567)
  es.sim = genSimData.BayesNormal(nCpGs = 100, 
    nCases = 20, nControls = 20,
    mu.n = -2, mu.c = 2,
    d0 = 20, s02 = 0.64, s02.c = 1.5, testPara = "var",
    outlierFlag = FALSE, 
    eps = 1.0e-3, applier = lapply) 
  print(es.sim)

  densityPlots(
    es = es.sim, 
    requireLog2 = FALSE, 
    myxlab = "expression level", 
    mymain = "density plots", 
    datExtrFunc = exprs, 
    fileFlag = FALSE, 
    fileFormat = "ps", 
    fileName = "densityPlots.ps")
  

iCheck documentation built on Nov. 1, 2018, 4:23 a.m.