bandle-prior: Computes the Kullback-Leibler divergence between Polya-Gamma...

In ococrook/bandle: An R package for the Bayesian analysis of differential subcellular localisation experiments

Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors

Description

Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors

Compute the KL divergence between two Dirichlet distributions

A function to compute the prior predictive distribution of the Dirichlet prior.

A function to compute the prior predictive distribution of the Polya-Gamma prior.

Usage

kldirpg(sigma = diag(1, 1, 1), mu = c(0, 0, 0), alpha = c(1))

kldir(alpha, beta)

prior_pred_dir(object, fcol = "markers", iter = 5000, dirPrior = NULL, q = 15)

prior_pred_pg(
  objectCond1,
  objectCond2,
  fcol = "markers",
  tau = 0.2,
  lambda = 0.01,
  mu_prior = NULL,
  iter = 10000,
  q = 15
)

Arguments

sigma	the sigma parameter of the Polya-Gamma prior. A positive-definite symmetric matrix.
mu	the mu parameter of the Polya-Gamma prior. A vector of means
alpha	The concentration parameter of the first Dirichlet distribution
beta	The concentration parameter of the second Dirichlet distribution
object	An instance of class MSnSet
fcol	The feature column indiating the markers. Default is "markers"
iter	Number of sample to use from prior predictive distribution. Default is 10000
dirPrior	The Dirichlet prior used. If NULL (default) will generate a a default Dirichlet prior. This should be a matrix with the same dimensions as the number of subcellular niches. The diagonal terms correspond to the prior probability of not differentially localising. The (i,j) term corresponds to prior probability of differntially localising between niche i and j.
q	The upper tail value. That is the prior probability of having more than q differential localisations. Default is 15.
objectCond1	An instance of class MSnSet, usually the control dataset
objectCond2	An instance of class MSnSet, usually the treatment dataset
tau	The tau parameter of the Polya-Gamma prior. Default is 0.2.
lambda	The lambda ridge parameter used for numerical stability. Default is 0.01
mu_prior	The mean of the Polya-Gamma prior. Default is NULL which generates a default Polya-Gamma prior.

Value

returns a numeric indicating the KL divergence

a numeric indicating the KL divergence

A list contain the prior predictive distribution of differential localisations, the mean number of differential localised proteins and the probability than more than q are differentially localised

A list contain the prior predictive distribution of differential localisations, the mean number of differential localised proteins and the probability than more than q are differentially localised

Examples

kldirpg(sigma = diag(c(1,1,1)), mu = c(0,0,0), alpha = 1)

kldir(c(1,1), c(3,1))

library(pRolocdata)
data("tan2009r1")

out <- prior_pred_dir(object = tan2009r1)

library(pRolocdata)
data("tan2009r1")
set.seed(1)
tansim <- sim_dynamic(object = tan2009r1, 
                    numRep = 6L,
                   numDyn = 100L)
d1 <- tansim$lopitrep
control1 <- d1[1:3]
treatment1 <- d1[4:6]
out <- prior_pred_pg(objectCond1 = control1[[1]],
objectCond2 = treatment1[[1]])

ococrook/bandle documentation built on Nov. 4, 2024, 12:27 a.m.