Summarize.Taxa: Summarize.Taxa Make taxa summary tables similar to QIIME...
In jbisanz/MicrobeR: Handy functions for microbiome analysis in R
Description
Usage
Arguments
Value
Description
Summarize.Taxa
Make taxa summary tables similar to QIIME summarize_taxa.py. Summarizes through the first 7 levels of taxonomy of OTUs/SVs wherein the levels are labeled as:
1-Kingdom
2-Phylum
3-Class
4-Order
5-Family
6-Genus
7-Species
8- Features with full taxonomy strings
Usage
1
SummarizedTaxa<-Summarize.Taxa(SVtable, TaxTable)
Arguments
FEATURES
Table of feature/OTU/SV COUNTS where Samples are columns, and IDs are row names
TAXONOMY
Table of taxonomies to aggregate on as identified above wherein the column names correspond to the taxonomic level
Value
A Named List of data frames of each level. Access by like TABLE$Genus or TABLE[[i]] where i is taxonomic level above.
jbisanz/MicrobeR documentation built on June 5, 2019, 7:53 p.m.
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Description Usage Arguments Value
Description
Summarize.Taxa
Make taxa summary tables similar to QIIME summarize_taxa.py. Summarizes through the first 7 levels of taxonomy of OTUs/SVs wherein the levels are labeled as:
1-Kingdom
2-Phylum
3-Class
4-Order
5-Family
6-Genus
7-Species
8- Features with full taxonomy strings
Usage
1 | SummarizedTaxa<-Summarize.Taxa(SVtable, TaxTable)
|
Arguments
FEATURES |
Table of feature/OTU/SV COUNTS where Samples are columns, and IDs are row names |
TAXONOMY |
Table of taxonomies to aggregate on as identified above wherein the column names correspond to the taxonomic level |
Value
A Named List of data frames of each level. Access by like TABLE$Genus or TABLE[[i]] where i is taxonomic level above.
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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