Description Usage Arguments Value Examples
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
1 2 3 4 5 | 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)
|
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 |
A sample from the posterior distribution in coda compatible format
1 2 3 4 5 6 7 8 9 | # 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.