plotSamplep95p05: Plot trajectories of the ratio of 95th percentile to 5th...

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

Description

Plot trajectories of the ratio of 95th percentile to 5th percentile of sample probe profiles across arrays.

Usage

plotSamplep95p05(
    es, 
    labelVariable = "subjID", 
     hybName = "Hybridization_Name",
    requireLog2 = FALSE, 
    projectName = "test", 
    plotOutPutFlag = FALSE, 
    cex = 1, 
    ylim = NULL, 
    xlab = "", 
    ylab = "", 
    lwd = 1.5, 
    mar = c(10, 4, 4, 2) + 0.1, 
    las = 2, 
    cex.axis=1.5,
    title = "Trajectory of p95/p05",
    cex.legend = 1.5,
    cex.lab = 1.5,
    legendPosition = "topright",
    cut1 = 10,
    cut2 = 6,
    sortFlag = TRUE,
    varSort = c("Batch_Run_Date", "Chip_Barcode", "Chip_Address"), 
    timeFormat = c("%m/%d/%Y", NA, NA),
    verbose = FALSE,
    ...)

Arguments

es	ExpressionSet object of Sample probe profiles.
labelVariable	A character string. The name of a phenotype data variable use to label the arrays in the boxplots. By default, labelVariable = "subjID" which is equivalent to labelVariable = "Hybridization_Name".
hybName	character string. indicating the phenotype variable Hybridization_Name.
requireLog2	logical. requiredLog2=TRUE indicates probe expression levels will be log2 transformed. Otherwise, no transformation will be performed.
projectName	A character string. Name of the project. The plots will be saved as pdf format files, the names of which have the format projectName_probeName_traj_plot.pdf.
plotOutPutFlag	logical. plotOutPutFlag=TRUE indicates the plots will be output to pdf format files. Otherwise, the plots will not be output to external files.
cex	numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. see par.
ylim	Range of y axis.
xlab	Label of x axis.
ylab	Label of y axis.
lwd	The line width, a _positive_ number, defaulting to '1'. see par.
mar	A numerical vector of the form 'c(bottom, left, top, right)' which gives the number of lines of margin to be specified on the four sides of the plot. The default is 'c(5, 4, 4, 2) + 0.1'. see par.
las	'las' numeric in 0,1,2,3; the style of axis labels. 0 - always parallel to the axis, 1 - always horizontal, 2 - always perpendicular to the axis, or 3 - always vertical. see par.
cex.axis	The magnification to be used for axis annotation relative to the current setting of cex. see par.
title	Figure title.
cex.legend	Font size of legend text.
cex.lab	The magnification to be used for x and y labels relative to the current setting of cex.
legendPosition	Position of legend. Possible values are “bottomright”, “bottom”, “bottomleft”, “left”, “topleft”, “top”, “topright”, “right” and “center”.
cut1	second horiztonal line setting the cutoff for the ratio p95/p05. A ratio above this line indicates the corresponding array is good.
cut2	second horiztonal line setting the cutoff for the ratio p95/p05. A ratio below this line indicates the corresponding array is bad.
sortFlag	logical. Indicates if arrays need to be sorted according to Batch_Run_Date, Chip_Barcode, and Chip_Address.
varSort	A vector of phenotype variable names to be used to sort the samples of es.
timeFormat	A vector of time format for the possible time variables in varSort. The length of timeFormat should be the same as that of varSort. For non-time variable, the corresponding time format should be set to be equal to NA. The details of the time format for time variable can be found in the R function strptime.
verbose	logical. Determine if intermediate output need to be suppressed. By default verbose=FALSE, intermediate output will not be printed.
...	Arguments to be passed to plot.

Details

The trajectory of the ratio of 95 to 5

Value

A list of 2 elements. The first element is the 2 x n matrix, where n is the number of arrays. The first row of the matrix is the 5-th percentile and the second row of the matrix is the 95-th percentile.

The second element is the ratio of the 95-th percentile to the 5-th percentile.

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)

  es.sim$Batch_Run_Date = 1:ncol(es.sim)
  es.sim$Chip_Barcode = 1:ncol(es.sim)
  es.sim$Chip_Address = 1:ncol(es.sim)
  

 plotSamplep95p05(
  es = es.sim, 
  labelVariable = "subjID", 
  hybName = "memSubj",
  requireLog2 = FALSE, 
  projectName = "test", 
  plotOutPutFlag = FALSE, 
  title = "Trajectory of p95/p05",
  cex.legend = 0.5,
  legendPosition = "topright",
  sortFlag = TRUE,
  varSort = c("Batch_Run_Date", "Chip_Barcode", "Chip_Address"), 
  timeFormat = c("%m/%d/%Y", NA, NA),
  verbose = FALSE)

iCheck documentation built on Nov. 8, 2020, 11:09 p.m.