getG0: Obtain the consensus null

View source: R/F_getG0.R

getG0R Documentation

Obtain the consensus null

Description

Obtain the consensus null

Usage

getG0(
  statObs,
  statsPerm,
  z0Quant,
  gridsize,
  maxIter,
  tol,
  estP0args,
  testPargs,
  B,
  p,
  pi0,
  assumeNormal,
  resamAssumeNormal
)

Arguments

statObs

A vector of lenght p with observed test statistics

statsPerm

A pxB matrix with permuation z-values

z0Quant

a vector of length of quantiles defining the central part R of the distribution. If a single number is supplied, then (z0quant, 1-z0quant) will be used

gridsize

An integer, the gridsize for the density estimation

maxIter

An integer, the maximum number of iterations in determining R

tol

The convergence tolerance.

estP0args

A list of arguments passed on to the estP0args() function

testPargs

A list of arguments passed on to quantileFun

B

an integer, the number of permutations

p

an integer, the number of hypotheses

pi0

A known fraction of true null hypotheses

assumeNormal

A boolean, should normality be assumed for the null distribution?

resamAssumeNormal

A boolean, should normality be assumed for resampling dists

Value

A list with following entries

PermDensFits

The permutation density fits

zSeq

The support of the kernel for density estimation

zValsDensObs

The estimated densities of the observed z-values

convergence

A boolean, has the algorithm converged?

weights

Vector of length B with weights for the permutation distributions

fdr

Estimated local false discovery rate along the support of the kernel

p0

The estimated fraction of true null hypotheses

iter

The number of iterations

fitAll

The consensus null fit


CenterForStatistics-UGent/reconsi documentation built on Nov. 13, 2023, 2:04 a.m.