sum_to_genus: Sum OTU data to the genus level
In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances
View source: R/singleSpec_contributions.R
sum_to_genus R Documentation
Sum OTU data to the genus level
Description
Needs Greengenes 97_otu_taxonomy.txt to be in the same directory
Usage
sum_to_genus(contribs, valueVar, taxonomy)
Arguments
contribs
metagenome_contributions output of PICRUSt
valueVar
"relAbundSample" or "singleMusicc", abundance metric to use for single taxon gene abundances
taxonomy
table of taxonomic classifications for OTUs, with either a "Genus" column or a Greengenes-formatted taxonomy column
Value
contribs added to the genus level
borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.
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View source: R/singleSpec_contributions.R
| sum_to_genus | R Documentation |
Sum OTU data to the genus level
Description
Needs Greengenes 97_otu_taxonomy.txt to be in the same directory
Usage
sum_to_genus(contribs, valueVar, taxonomy)
Arguments
contribs |
metagenome_contributions output of PICRUSt |
valueVar |
"relAbundSample" or "singleMusicc", abundance metric to use for single taxon gene abundances |
taxonomy |
table of taxonomic classifications for OTUs, with either a "Genus" column or a Greengenes-formatted taxonomy column |
Value
contribs added to the genus level
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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