dpeaqms.mcmc: dpeaqms MCMC Sampling function

In dpeaqms: Differential Protein Expression Analysis using Quantitative Mass Spectrometry Data (dpeaqms)

Description

A function that will take an MS/MS data object and run an MCMC algorithm to sample from the posterior distribution of the model (see dpeaqms.model) parameters

Usage

  dpeaqms.mcmc(msmsdata, burnin, samples, thin,
               a.alpha, b.alpha, a.gamma,  b.gamma,
               a.tau, b.tau,a.kappa, b.kappa, 
               a.p, b.p, controlGroup, referenceSampleID, 
	       transform, infofilename, verbose, seed)

Arguments

msmsdata	A data frame containing the MS/MS data. The data frame should have the columns: "experiment", "protein", "msmsID", "intensity", "sample" and "group".
burnin	The number of initial MCMC iterations to be discarded.
samples	The number of samples to take from the MCMC chain.
thin	This is the thinning interval on the sampled MCMC chain i.e. the interval between consecutive samples
a.alpha	The mean of the Gaussian prior distribution on the model parameter alpha (See model description)
b.alpha	The precision of the Gaussian prior distribution on the model parameter alpha (See model description)
a.gamma	The mean of the Gaussian prior distribution on the model parameter gamma (See model description)
b.gamma	The precision of the Gaussian prior distribution on the model parameter alpha (See model description)
a.tau	The shape parameter of the Gamma prior distribution on the model parameter tau (See model description)
b.tau	The rate parameter of the Gamma prior distribution on the model parameter tau (See model description)
a.kappa	The mean of the Gaussian prior distribution on the model parameter kappa (See model description)
b.kappa	The precison of the Gaussian prior distribution on the model parameter kappa (See model description)
a.p	First parameter of the Beta hyperprior distribution on the parameter p
b.p	Second parameter on the Beta hyperprior distribution on the the model parameter p
controlGroup	The label of the group to be used as the control. By default the first group label is used as the control
referenceSampleID	A list of labels of the samples to be used as the calibration channel (one for each experiment). If none is specified the first sample label in each experiment is used.
transform	If TRUE uses the log of the reporter ion intensities otherwise leaves the intensities unchanged
infofilename	Specifies the name of the file to which to output the parameters used in the MCMC run
verbose	Print out information on the run progress
seed	Always the user to set the seed of the RNG used by JAGS for reproducible output

Value

A sample from the posterior distribution in coda compatible format

Examples

  # Load the dpeaqms library
  library(dpeaqms)

  # Load the simulated dataset that comes with the package
  data(dpeaqms.simulatedDataset1)
  simdata <- dpeaqms.simulatedDataset1
  # Sample from the posterior distribution of the model
  simdataSamples <- dpeaqms.mcmc(msmsdata=simdata, transform=FALSE,
                                 samples=100, thin=10, burnin=1000)

dpeaqms documentation built on May 2, 2019, 4:46 p.m.