jade_permute: Run JADE with permuted group assignments

In jean997/jadeTF:

Description

This function takes the complete data matrix and re-runs JADE permuting the group labels. It can optionally recalculate the weights in the likelihood.

Usage

jade_permute(Y, fit0, gammas, save.prefix, sample.size = NULL, tol = 0.001,
  which.perm = 1:100, sds.mat = NULL, n.rep.fit.var = NULL,
  adjust.rho.alpha = TRUE, sd.type = c("Mat2", "Binomial", "Poisson",
  "EqualFromData", "Mat", "Orig"), READS = NULL)

Arguments

Y	Full data matrix (p by n)
fit0	A JADE fit using original group labels at gamma=0
gammas	List of gammas at which to fit permutation fits
tol	Tolerance for declaring sites separated
n.rep.fit.var	If NULL use original fit.var. Otherwise the number of bootstrap replications to use.
sd.type	If "Orig" use sds used in fit0. Otherwsie recalculated sds for each permutation assuming binomial or poisson models.
READS	Required if sd.type="Binomial"
n.perm	Number of permutations

Value

A list with elements #'

sep.total

A matrix length(gammas) by h n.perm

gammas

Gamma values fit for each permutation

tol

The tolerance at which the seaparation in sep.total and sep were calculated

jean997/jadeTF documentation built on May 18, 2019, 11:44 p.m.