summarize.sum: Sum-based probe summarization

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

Sum-based probe summarization

Description

Probeset summarization with the standard sum method.

Usage

summarize.sum(
  taxonomy,
  level,
  probedata,
  verbose = TRUE,
  downweight.ambiguous.probes = TRUE
)

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
downweight.ambiguous.probes	Downweight probes with multiple targets

Value

List with two elements: abundance.table (summarized data matrix in absolute scale) and probe.parameters used in the calculations

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation("microbiome")

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