Description Usage Arguments Details Value Author(s) References Examples

This is the main function of the BGmix package. It calls the C++ code which performs the MCMC to fit the BGmix model.

1 2 3 4 5 6 7 8 | ```
BGmix(ybar, ss, nreps, neffects = 2, xx = matrix(c(1, 1, -0.5, 0.5),
ncol = 2, byrow = T), ntau = NULL, indtau = NULL, jstar = 1, niter =
10000, nburn = 10000, nthin = 10, seed = 12345, move.choice.bz = 4,
move.choice.aa = 1, move.choice.lam = 0, move.choice.tau = 1,
move.choice.eta = 1, trace.out = 1, trace.pred = 0, sig.aa = 0.1,
tau.eps = 50, lambda.up.init=1.5, lambda.down.init=1.5,
datafilename.ybar = NULL, xfilename = NULL, itfilename =
NULL, rundir=".")
``` |

`ybar` |
matrix no. genes x no. experimental conditions. Mean log gene expression for each gene in each condition. |

`ss` |
matrix no. genes x no. experimental conditions. Sample variance of log gene expression for each gene in each condition. |

`nreps` |
vector containing the number of replicate arrays in each experimental condition |

`neffects` |
number of effect parameters per gene (eg. 2 for unpaired differential expression) |

`xx` |
design matrix: no. effects x no. experimental conditions. See Vignette for specification of design matrix. Default is for unpaired differential expression. |

`ntau` |
number of variances per gene |

`indtau` |
label for each condition indicating which variance grouping that condition belongs to. See Vignette for more detail. |

`jstar` |
Label of the effect parameter which has the mixture prior. Labels start at 0, as in C++. If no parameter has a mixture prior, set jstar=-1. |

`niter` |
no. MCMC iterations after burn-in. This must be at least 100 for the function to work (or else set to zero). |

`nburn` |
no. MCMC iterations for burn-in. This must be at least 100 for the function to work (or else set to zero). |

`nthin` |
thinning parameter for MCMC iterations |

`seed` |
initial value for random seed |

`move.choice.bz` |
indicates choice of mixture prior: 1 for point mass null + Uniform alternatives, 4 for point mass null + Gamma alternatives, 5 for small Normal null + Gamma alternatives |

`move.choice.aa` |
if this is 1, hyperparameter a for gene variances is updated, if this is 0 it is fixed. |

`move.choice.lam` |
if this is 1, hyperparameter lambda for mixture prior is updated, if this is 0 it is fixed. |

`move.choice.tau` |
indicates choice of prior on gene variances: 1 for Inverse Gamma, 2 for log Normal. |

`move.choice.eta` |
if this is 1, hyperparameter eta for mixture prior is updated, if this is 0 it is fixed. |

`trace.out` |
if this is 1, output trace of model parameters, if this is 0, no output. |

`trace.pred` |
if this is 1, output trace of predictive quantities, if this is 0, no output. |

`sig.aa` |
step-size in random walk update for a (hyperparameter for gene variances distribution) |

`tau.eps` |
Value of epsilon used in the small Normal null mixture component. |

`lambda.up.init` |
init or fixed value of lambda+ (parameter of Gamma mixture component) |

`lambda.down.init` |
init or fixed value of lambda- (parameter of Gamma mixture component) |

`datafilename.ybar` |
character. Name describing the data set (by default this is taken from the name of the ybar argument). |

`xfilename` |
character. Name describing the design matrix. |

`itfilename` |
character. Name describing the indtau parameter. |

`rundir` |
character. Path for saving output files. A new
sub-directory is created in the |

The C++ code writes a count down on the screen, to give an indication of how long the code has to run. Output is written to a sub-directory of the working directory. This sub-directory is created automatically, and its name is printed by the C++ code to the screen.

The output directory is returned (character).

Alex Lewin

Lewin, A., Bochkina, N. and Richardson, S. (2007), Fully Bayesian mixture model for differential gene expression: simulations and model checks. http://www.bgx.org.uk/publications.html

1 2 3 4 |

BGmix documentation built on May 2, 2018, 3:11 a.m.

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