estimate.hyperparameters {RPA} | R Documentation |
Hyperparameter estimation.
estimate.hyperparameters(sets = NULL, probe.parameters = list(alpha = 2, beta = 1), batches, cdf = NULL, bg.method = "rma", epsilon = 0.01, load.batches = FALSE, save.hyperparameter.batches = FALSE, mc.cores = 1, verbose = TRUE, normalization.method = "quantiles", save.batches.dir = ".", unique.run.identifier = NULL, set.inds = set.inds)
sets |
Probesets to handle. All probesets by default. |
probe.parameters |
User-defined priors. May also include quantile.basis |
batches |
Data batches for online learning |
cdf |
CDF probeset definition file |
bg.method |
Background correction method |
epsilon |
Convergence parameter |
load.batches |
Logical. Load preprocessed data whose identifiers are picked from names(batches). Assuming that the same batch list (batches) was used to create the files in online.quantiles function. |
save.hyperparameter.batches |
Save hyperparameters for each batch into files using the identifiers with batch name with -hyper.RData suffix. |
mc.cores |
Number of cores for parallel computation |
verbose |
Print progress information |
normalization.method |
Normalization method |
save.batches.dir |
Specify the output directory for temporary batch saves. |
unique.run.identifier |
Define identifier for this run for naming the temporary batch files. By default, a random id is generated. |
set.inds |
Probeset indices |
alpha: Hyperparameter alpha (same for all probesets); betas: Hyperparameter beta (probe-specific); variances: Probe-specific variances (beta/alpha)
Leo Lahti leo.lahti@iki.fi
See citation("RPA")
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