ecdfAUC: Draw Empirical Cumulative Density Function (ECDF) plot

In sSeq: Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

Description

This function is used to draw Empirical CDF plot. It relies on the trapz function in the caTools package. A user needs to install the caTool library first.

Usage

ecdfAUC(dd, col.line=NULL, main="ECDF", cex.leg=1, drawRef=FALSE, 
       rm1=FALSE, lineType=NULL, addLeg=TRUE, xlab="p-value", 
       ylab="ECDF", cex.axis=1.5, cex.main=1.8, cex.lab=1.2, 
      axis.padj=c(-1, 1), lab.padj=c(-1.5, 1), lwd=1, box.lwd=1.2)

Arguments

dd	A data frame of p-values in which a column represents the p-values or posterior probabilities resulted by a method.
col.line	A vector of color characters. The default is NULL and this function automatically assigns the color for each cover shown in the ECDF plot.
main	The title of the plot.
cex.leg	An integer specifying size of the legend in the the plot.
drawRef	If TRUE, then a gray 45 degree line will be added in the plot.
rm1	If users believe that the p-values equal to 1 belong to the different group of the others, and want to exclude them from the calculation of empirical CDF, then use rm1=TRUE.
lineType	A vector of integers indicating the type of lines used for the methods.
addLeg	If “TRUE" then a legend box with legend is added to the figure.
xlab	Label of x axis.
ylab	Label of y axis.
cex.axis	The size of labels on the axes.
cex.main	A characteristic string indicating the size of the main.
cex.lab	The size for the labels on x and y.
axis.padj	The perpendicular adjustment of ticks.
lab.padj	The perpendicular adjustment of labels for an axix.
lwd	The width of the line shown in a figure.
box.lwd	The width of the box line in a figure.

Examples

x<-data.frame(A=runif(100), B=rbeta(100, 0.5, 1.2))
ecdfAUC(x);

Example output

Loading required package: caTools
Loading required package: RColorBrewer
        A         B 
0.5549111 0.7321791 

sSeq documentation built on Nov. 8, 2020, 5:52 p.m.