local.fdr {RFlocalfdr}

local fdr

Description

calculate the local

Usage

local.fdr(
  f,
  x,
  FUN = my.dsn,
  p0 = 1,
  debug.flag = 0,
  plot.string = "",
  temp.dir = NULL,
  ...
)

Arguments

f

object retuned by call to f.fit

x

f_fit$midpoints

FUN

my.dsn

p0

estimated proportion of null importances

debug.flag

either 0 (no debugging information), 1 or 2

plot.string

file name for a debugging plot

temp.dir

directory for debugging output

...

arguments passed to FUN

Value

returns an estimate of the local false discovery rate.

Examples

data(imp20000)                                      
imp<-log(imp20000$importances)                               
t2<-imp20000$counts
temp<-imp[t2 > 1]   #see                          
temp<-temp[temp != -Inf]                         
temp <- temp - min(temp) + .Machine$double.eps   
f_fit <- f.fit(temp)                             
y <- f_fit$zh$density                            
x <- f_fit$midpoints                             
df <- data.frame(x, y)                           
fitted_parameters <- fit.to.data.set(df, temp, try.counter = 3)           
fitted_parameters

aa <- local.fdr(f_fit, df$x, FUN = my.dsn, xi = fitted_parameters$Estimate[1],
                omega = fitted_parameters$Estimate[2], lambda = fitted_parameters$Estimate[3],
                debug.flag = 0, plot.string = "initial")

plot(x,y,axes=FALSE,type="l",col="blue",main = "local fdr",
      xlab="importances",ylab="")                                                                                       
axis(2, pretty( c(0,max(y)+0.5*max(y)),10))                                                                            
                                                                                                                        
oldpar <- par(new = TRUE)
plot(x, aa, type="l",col="green",main = "",xlab="",ylab="",axes=FALSE)                                                 
abline(h = 0.2)                                                                                                        
axis(4, pretty( aa,10))                                                                                                
                                                                                                                        
axis(1,pretty(x,10))                                                                                                   
box() #- to make it look "as usual                                                                                     
legend("topright",c("density importances","local fdr"),col=c("blue","green"),lty=1)
par(oldpar)


library(RFlocalfdr.data)
data(ch22)                                                                                                             
imp<-log(ch22$imp)
t2<-ch22$C                                                                                                             
imp<-imp[t2 > 30]                                                                                                      
imp <- imp - min(imp) + .Machine$double.eps                                                                            
debug.flag <- 0                                                                                                        
f_fit <- f.fit(imp, debug.flag = debug.flag)                                                                           
y <- f_fit$zh$density                                                                                                  
x <- f_fit$midpoints                                                                                                   
df <- data.frame(x, y)                                                                                                 
initial.estimates <- fit.to.data.set.wrapper(df, imp, debug.flag = debug.flag,
return.all = FALSE)

aa <- local.fdr(f_fit, df$x, FUN = my.dsn, xi = initial.estimates$Estimate[1],
    omega = initial.estimates$Estimate[2], lambda = initial.estimates$Estimate[3],  debug.flag = 0,
                    plot.string = "initial")

plot(x,y,axes=FALSE,type="l",col="blue",main = "local fdr",                                                            
     xlab="importances",ylab="")                                                                                       
axis(2, pretty( c(0,max(y)+0.5*max(y)),10))                                                                            
                                                                                                                       
oldpar <- par(new = TRUE)
plot(x, aa, type="l",col="green",main = "",xlab="",ylab="",axes=FALSE)                                                 
abline(h = 0.2)                                                                                                        
axis(4, pretty( aa,10))                                                                                                
                                                                                                                       
axis(1,pretty(x,10))                                                                                                   
box() #- to make it look "as usual                                                                                     
legend("topright",c("density importances","local fdr"),col=c("blue","green"),lty=1)
par(oldpar)