densityPlots: Draw estimated density plots for all arrays

In iCheck: QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

Description

Draw estimated density plots for all arrays.

Usage

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 <[e-mail]>, Brandon Guo <[e-mail]>, Christopher Anderson <[e-mail]>, Barbara Klanderman <[e-mail]>, Vincent Carey <[e-mail]>, Benjamin Raby <[e-mail]>

Examples

  # 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. 8, 2020, 11:09 p.m.