summarize.sum: Sum-based probe summarization

summarize.sumR Documentation

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 microbiome-admin@googlegroups.com

References

See citation("microbiome")


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