histpvalueplotter {a4Base} | R Documentation |
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.
histpvalueplotter( pValue, addLegend = FALSE, xlab = NULL, ylab = NULL, main = NULL, ... )
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 |
no returned value, a plot is drawn to the current device.
Willem Talloen and Tobias Verbeke
histPvalue
, propdegenescalculation
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"]) }