summarize.rpa {RPA}R Documentation

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 microbiome-admin@googlegroups.com

References

See citation("microbiome")


[Package RPA version 1.42.0 Index]