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

summarize.batches

R Documentation

summarize.batches

Description

Summarize batches.

Usage

summarize.batches(
  sets = NULL,
  probe.parameters = list(),
  batches,
  load.batches = FALSE,
  mc.cores = 1,
  cdf = NULL,
  bg.method = "rma",
  normalization.method = "quantiles",
  verbose = TRUE,
  save.batches.dir = ".",
  unique.run.identifier = NULL,
  save.batches = FALSE,
  set.inds,
  speedup = FALSE,
  summarize.with.affinities = FALSE
)

Arguments

`sets`	Probesets to summarize
`probe.parameters`	Optional probe parameters, including priors.
`batches`	Data batches for online learning
`load.batches`	Logical. Load precalculated data for the batches.
`mc.cores`	Number of cores for parallel computation
`cdf`	CDF for alternative probeset definitions
`bg.method`	Background correction method
`normalization.method`	Normalization method
`verbose`	Print progress information
`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.
`save.batches`	Save batches?
`set.inds`	Probeset indices
`speedup`	Speed up calculations with approximations.
`summarize.with.affinities`	Use affinity estimates in probe summarization step. Default: FALSE.