mcmc.bgx {bgx}R Documentation

Internal wrapper function for calling the bgx C++ function.

Description

This internal function calls the bgx method in a loaded bgx shared object (bgx.so/bgx.dll)

Usage

mcmc.bgx(pm, mm, samplesets, probesets, numberCategories, categories, unknownProbeSeqs, numberOfUnknownProbeSeqs, 
  numberGenesToWatch, whichGenesToWatch, whichProbesToWatch, iter, burnin,
  adaptive, batch_size=50, optimalAR=0.44, output, samplenames = "unknown",
  subsample = ifelse(iter > 1024, iter/1024, 1), seed = 192492, rundir)

Arguments

pm Perfect Match probes
mm MisMatch probes
samplesets A numeric vector specifying which condition each array belongs to. E.g. if samplesets=c(2,2), then the first two replicates belong to one condition and the last two replicates belong to another condition. If NULL, each array is assumed to belong to a different condition.
probesets A numeric vector specifying how probes are grouped into probesets.
numberCategories Number of probe affinity categories.
categories A numeric vector specifying which category each probe belongs to.
unknownProbeSeqs A numeric vector specifying which probes lack sequence information.
numberOfUnknownProbeSeqs Number of probes lacking sequence information.
numberGenesToWatch How many genes to monitor closely.
whichGenesToWatch A numeric vector specifying which genes to monitor closely.
whichProbesToWatch The starting position for each probe in each gene to monitor closely.
iter Number of post burn-in iterations.
burnin Number of burn-in iterations.
adaptive Use adaptive MCMC for better mixing.
batch_size Batch size for adaptive MCMC.
optimalAR Optimal acceptance ratio.
output One of "minimal", "trace", "diagnostic" or "mcse".
samplenames Vector of names for each array.
subsample Subsampling interval.
seed Seed for PRNG.
rundir The directory in which to place the output run directories.

Details

See bgx for more details.

Value

The name of the output directory.

Note

You shouldn't call this function directly, but if you do, make sure the appropriate shared object is loaded.

Author(s)

Ernest Turro

See Also

bgx, standalone.bgx


[Package bgx version 1.6.0 Index]