a4 (version 1.20.0)

histpvalueplotter: Workhorse function for the histPvalue function

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

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"])
}