Plot results of FDR table generated by fdrTbl()

This function plots FDR point and CI estimates over a sequence of possible significance thresholds. Results from fdrTbl() can be plotted directly as input to FDRplot.

FDRplot(plotdat, lowerbound, upperbound, ymax = 1, annot = "", xpos = 0.8,
  ypos = 0.8, outfile = FALSE)

Arguments

plotdat	a table that is returned from fdrTbl(), or results formated in the same way.
lowerbound	-log10(p-value) lower bound for the x-axis of the plot.
upperbound	-log10(p-value) upper bound for the x-axis of the plot.
ymax	upper limit for range of the y-axis.
annot	annotation text to be added to plot area.
xpos	x-axis position for annot
ypos	y-axis position for annot
outfile	either 'FALSE' or the path/name of a new pdf file to be generated by the function.

Value

ggplot2 object

References

Millstein J, Volfson D. 2013. Computationally efficient permutation-based confidence interval estimation for tail-area FDR. Frontiers in Genetics | Statistical Genetics and Methodology 4(179):1-11.

Millstein J, Volfson D. 2013. Computationally efficient permutation-based confidence interval estimation for tail-area FDR. Frontiers in Genetics | Statistical Genetics and Methodology 4(179):1-11.

Examples

ss = 100
nvar = 100
X = as.data.frame(matrix(rnorm(ss*nvar),nrow=ss,ncol=nvar))
Y = as.data.frame(matrix(rnorm(ss*nvar),nrow=ss,ncol=nvar))
nperm = 10

myanalysis = function(X,Y){
        ntests = ncol(X)
        rslts = as.data.frame(matrix(NA,nrow=ntests,ncol=2))
        names(rslts) = c("ID","pvalue")
        rslts[,"ID"] = 1:ntests
        for(i in 1:ntests){
                fit = cor.test(X[,i],Y[,i],na.action="na.exclude",
                        alternative="two.sided",method="pearson")
                rslts[i,"pvalue"] = fit$p.value
        }
        return(rslts)
} # End myanalysis

# Generate observed results
obs = myanalysis(X,Y)

# Generate permuted results
perml = vector('list',nperm)
for(p_ in 1:nperm){
        X1 = X[order(runif(nvar)),]
        perml[[p_]] = myanalysis(X1,Y)
}

# FDR results table
myfdrtbl = fdrTbl(obs$pvalue,perml,"pvalue",nvar,0,3)
# Plot results
FDRplot(myfdrtbl,0,3,annot="A. An Example")
#> Warning: Removed 8 rows containing missing values (geom_path).
#> Warning: Removed 8 rows containing missing values (geom_point).
#> Warning: Removed 8 rows containing missing values (geom_text).