View source: R/community_rrna.R
community_rrna | R Documentation |
Calculate the average 16S rRNA copy number for each sample in an OTU table
community_rrna(x, copy.database = "v13.5", weighted = TRUE)
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. |
A dataframe with an average copy number for each sample
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