summarize.batch: summarize.batch
In microbiome/RPA: RPA: Robust Probabilistic Averaging for probe-level analysis

summarize.batch

R Documentation

summarize.batch

Summarize batch.

summarize.batch(
  q,
  set.inds,
  probe.parameters = list(),
  epsilon,
  verbose = FALSE,
  mc.cores = 1,
  summarize.with.affinities = FALSE
)

`q`	Background corrected, quantile-normalized, log2 probes x samples matrix
`set.inds`	Indices for each probeset, corresponding to q matrix
`probe.parameters`	A list, each element corresponding to a probe set. Each probeset element has the following elements: affinity, variance and optionally alpha and beta priors. Each of these elements contains a vector over the probeset probes, specifying the probe parameters according to the RPA model. If variances are given, that overrides the priors.
`epsilon`	Convergence tolerance. The iteration is deemed converged when the change in all parameters is < epsilon.
`verbose`	Print progress information during computation.
`mc.cores`	Number of cores for parallel processing
`summarize.with.affinities`	Use affinity estimates in probe summarization step. Default: FALSE.