summarize.by.level: Sum the sequences that belong to the same taxon.
In gabrielrfernandes/tagme: Taxonomic Assignment of Genetic Markers for Ecology
Description
Usage
Arguments
Value
Description
Sum the sequences that belong to the same taxon.
Usage
1
2
summarize.by.level(count.table, taxonomy, level = "Genus",
taxa.are.rows = FALSE)
Arguments
count.table
The count table containing the quantification for each sequence.
taxonomy
The taxonomic assignment produced by TAG.ME.
level
The The taxon level to be summarized. Values are: "Domain", "Phylum", "Class", "Order", "Family", "Genus", or "Specie". Default value = "Genus". Default is FALSE.
taxa.are.rows
Boolean value describing your count table organization. TRUE value means that your table contains your sequences (ASVs, OTUs) as rownames, and your samples are colnames - Ex: OTU tables generated by Qiime. FALSE value means that your sequences are the colnames and samples are the rownames - Ex: Seqtable produced by Dada2.
Value
A count table with the unique taxons as rownames and the summarized count for each.
gabrielrfernandes/tagme documentation built on Dec. 25, 2021, 1:25 a.m.
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Description Usage Arguments Value
Description
Sum the sequences that belong to the same taxon.
Usage
1 2 | summarize.by.level(count.table, taxonomy, level = "Genus",
taxa.are.rows = FALSE)
|
Arguments
count.table |
The count table containing the quantification for each sequence. |
taxonomy |
The taxonomic assignment produced by TAG.ME. |
level |
The The taxon level to be summarized. Values are: "Domain", "Phylum", "Class", "Order", "Family", "Genus", or "Specie". Default value = "Genus". Default is FALSE. |
taxa.are.rows |
Boolean value describing your count table organization. TRUE value means that your table contains your sequences (ASVs, OTUs) as rownames, and your samples are colnames - Ex: OTU tables generated by Qiime. FALSE value means that your sequences are the colnames and samples are the rownames - Ex: Seqtable produced by Dada2. |
Value
A count table with the unique taxons as rownames and the summarized count for each.
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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