vlo: vlo

In jamesliley/cfdr: Implements cFDR testing with overall FDR control

Description

Return co-ordinates of L-regions using 'oracle' method in which PDFs of ZP,ZQ|HP0 and ZP,ZQ are known

Usage

vlo(p, q, f0, f, indices = NULL, at = NULL, nt = 5000, nv = 1000,
  scale = c("p", "z"), closed = T)

Arguments

p	principal p-values
q	conditional p-values
f0	PDF of ZP,ZQ|HP0. Function of two variables. Can also be CDF if oracle cFDR is wanted instead of cfdr.
f	PDF of ZP,ZQ. Function of two variables. Can also be CDF if oracle cFDR is wanted instead of cfdr.
indices	instead of at cfdr cutoffs, compute v(L) at indices of points. Overrides parameter at if set.
at	cfdr cutoff/cutoffs. Defaults to null
nt	number of test points in x-direction, default 5000
nv	resolution for constructing L-curves, default 1000
scale	return curves on the p- or z- plane. Y values are equally spaced on the z-plane.
closed	determines whether curves are closed polygons encircling regions L (closed=T), or lines indicating the rightmost border of regions L

Value

list containing elements x, y. Assuming n curves are calculated (where n=length(indices) or length(at)) and closed=T, x is a matrix of dimension n x (4+nv), y ix a vector of length (4+nv).

Author(s)

James Liley

Examples

# Generate standardised simulated dataset
set.seed(1); n=10000; n1p=100; n1pq=100; n1q=100
zp=c(rnorm(n1p,sd=3), rnorm(n1q,sd=1),rnorm(n1pq,sd=3), rnorm(n-n1p-n1q-n1pq,sd=1))
zq=c(rnorm(n1p,sd=1), rnorm(n1q,sd=3),rnorm(n1pq,sd=3), rnorm(n-n1p-n1q-n1pq,sd=1))
p=2*pnorm(-abs(zp)); q=2*pnorm(-abs(zq))
fold_id=(1:n) %% 3


# points to generate L-regions for
example_indices=c(4262, 268,83,8203)


v1=vlo(p,q,f0,f,indices=example_indices); 
plot(p,q,cex=0.5,col="gray",xlim=c(0,0.001),ylim=c(0,1), main="Oracle rejection regions"); 
for (i in 1:length(example_indices)) lines(v1$x[i,],v1$y); 
for (i in 1:length(example_indices)) points(p[example_indices[i]],q[example_indices[i]],qh=16,col="blue")

jamesliley/cfdr documentation built on July 31, 2020, 9:42 a.m.