community_rrna: Calculate the community/sample-wise mean 16S rRNA copy...

Description Usage Arguments Value

View source: R/community_rrna.R

Description

Calculate the average 16S rRNA copy number for each sample in an OTU table

Usage

1
community_rrna(x, copy.database = "v13.5", weighted = TRUE)

Arguments

x

A phyloseq object OR an OTU-table with taxa as rows and OTU names as rownames. OTUs should be picked against the Greengenes v13.5 database, unless a another copy number database is provided.

copy.database

What Greengenes database version was used to find OTUs. Atm only "v13.5" is available. Alternatively, A dataframe with two variables: "ID" is the OTU id matched by rownames in x and "Copy" is the copy number.

weighted

Logical. Should the average copy number be weighted by the relative abundances of the OTUs? If not, it is adviced to rarefy the otu-table first if there are large differences in sample reads.

Value

A dataframe with an average copy number for each sample


Russel88/MicEco documentation built on Oct. 24, 2018, 3:07 p.m.