histpvalueplotter: Workhorse function for the histPvalue function

In a4Base: Automated Affymetrix Array Analysis Base Package

Description

Workhorse function for the histPvalue function. This function displays the distribution of the p values using a histogram; the horizontal line represents a uniform distribution based on the p value distribution between 0.5 and 1. This represents the hypothetical p value distribution arising just by chance. This uniform distribution is used to estimate the proportion of differentially expressed genes.

Usage

histpvalueplotter(
  pValue,
  addLegend = FALSE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  ...
)

Arguments

pValue	numeric vector of p values
addLegend	logical; should a legend be added (TRUE) or not (FALSE; default
xlab	label for the x axis; defaults to NULL (no label)
ylab	label for the y axis; defaults to NULL (no label
main	main title for the plot; if NULL (default) no main title is displayed
...	further arguments for the hist call; currently none are used

Value

no returned value, a plot is drawn to the current device.

Author(s)

Willem Talloen and Tobias Verbeke

See Also

histPvalue, propdegenescalculation

Examples

 if (require(ALL)){
   data(ALL, package = "ALL")
   ALL <- addGeneInfo(ALL)
   ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
   tTestResult <- tTest(ALL, "BTtype")
   histPvalue(tTestResult[,"p"], addLegend = TRUE, xlab = "Adjusted P Value")
   histPvalue(tTestResult[,"p"], addLegend = TRUE, main = "Histogram of Adjusted P Values")
   propDEgenesRes <- propDEgenes(tTestResult[,"p"])
 }

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.