summarize.rpa: RPA summarization

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

RPA summarization

Description

Probeset summarization with RPA for taxonomic data.

Usage

summarize.rpa(
  taxonomy,
  level,
  probedata,
  verbose = TRUE,
  probe.parameters = NULL
)

Arguments

taxonomy	oligo - phylotype matching data.frame
level	taxonomic level for the summarization.
probedata	preprocessed probes x samples data matrix in absolute domain
verbose	print intermediate messages
probe.parameters	Optional. If probe.parameters are given, the summarization is based on these and model parameters are not estimated. A list. One element for each probeset with the following probe vectors: affinities, variances

Value

List with two elements: abundance.table (summarized data matrix in absolute scale) and probe.parameters (RPA probe level parameter estimates)

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation("microbiome")

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