summarize_taxonomy: Summarize taxonomy

Description Usage Arguments Value

View source: R/microbiome_helpers.R

Description

Summarize a specified taxonomy within a higher level, usually phylum

Usage

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summarize_taxonomy(physeq, grouping_tax = "Phylum",
  summary_tax = "Genus", filter = 0.01)

Arguments

physeq

a valid phyloseq object

grouping_tax

the higher level taxonomy to group within

summary_tax

the lower level taxonomy to summarize

filter

numeric, filter out members of the summary taxonomy below this fraction

Value

a data frame


mworkentine/mattsUtils documentation built on May 23, 2019, 11:58 a.m.