frpa: frpa

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

frpa

Description

Frozen-RPA preprocessing using precalculated probe parameters.

Usage

frpa(
  abatch = NULL,
  probe.parameters = NULL,
  verbose = FALSE,
  cdf = NULL,
  cel.files = NULL,
  cel.path = NULL,
  mc.cores = 1,
  summarize.with.affinities = FALSE
)

Arguments

abatch	An AffyBatch object.
probe.parameters	A list with tau2 (probe variance), quantile.basis (basis for quantile normalization in log2 domain), and optionally affinity (probe affinities). The probe.parameters$tau2 and probe.parameters$affinity are lists, each element corresponding to a probeset and containing a parameter vector over the probes. The quantile.basis is a vector over the probes, the probes need to be listed in the same order as in tau2 and affinity. probe.parameters can be optionally provided as a data frame.
verbose	Print progress information during computation.
cdf	Specify an alternative CDF environment. Default: none.
cel.files	List of CEL files to preprocess.
cel.path	Path to CEL file directory.
mc.cores	Number of cores for parallelized processing.
summarize.with.affinities	Use affinity estimates in probe summarization step. Default: FALSE.

Details

fRPA function to preprocess Affymetrix CEL files with RPA using precalculated (frozen) probe parameters.

Value

Preprocessed expression matrix in expressionSet format

Author(s)

Leo Lahti [e-mail]

References

See citation("RPA")

See Also

rpa, AffyBatch, ExpressionSet

Examples

# eset <- frpa(abatch, probe.parameters)

microbiome/RPA documentation built on April 9, 2023, 10:59 a.m.