agg_otus: Aggregate OTU data by another taxonomic level.

In cb-42/cbmbtools: R Functions for Facilitating Microbiome Analyses

Description

Aggregate OTU data by another taxonomic level.

Usage

agg_otus(
  df = otu_df,
  sample_col = NULL,
  tax_df = otu_good_taxonomy,
  taxon = "Phylum"
)

Arguments

df	A dataframe containing OTU data, presumed to be normalized, although it could be done for raw count data as well. Defaults to otu_df.
sample_col	An optional vector, specifying the column in df which contains Sample names. If none is provided and a Sample_name column does not exist, rownames will be used.
tax_df	Taxonomy table. agg_otus() assumes that a column called OTU exists in tax_df. Defaults to otu_good_taxonomy.
taxon	String which describes the taxonomic level to aggregate by. Default is "Phylum".

Value

An aggregated tibble containing a column of Sample names and columns named according to the levels in taxon.

Examples

phy_df <- agg_otus(otu_df, "Phylum")

cb-42/cbmbtools documentation built on Jan. 9, 2021, 1:38 a.m.