Package description
You can install TAG.ME in your R environment.
You will need the devtools library.
library(devtools)
If you do not have devtools installed, you can install it now, and the load it
install.packages("devtools")
library(devtools)
Now you can install TAG.ME from the Github repository
install_github("gabrielrfernandes/tagme")
library(tagme)
tagmeFromFasta
Description
Assign taxonomy to an input FASTA file.
Usage
tagmeFromFasta(file, db = "./", specificity = 0.8, batch = 50000)
Arguments
file |
The FASTA file to be classified. It can be a group of ASV, OTU or Unique sequences. |
db |
The directory containing the downloaded RDS and TXT files corresponding to your amplicon region. The directory name must end with "/". |
specificity |
The Specificity that will determine the threshold score for assignment. |
batch |
The maximum number of sequences to be assigned per batch. Bigger batches demand more memory. |
Value
A table containing the taxonomic assignment and the score to each sequence.
tagmeFromDADA2
Description
Assign taxonomy to an input Seqtab variable, exported from DADA2.
Usage
tagmeFromDADA2(seqtab, db = "./", specificity = 0.8, batch = 50000)
Arguments
seqtab |
The seqtab object produced by DADA2. |
db |
The directory containing the downloaded RDS and TXT files corresponding to your amplicon region. The directory name must end with "/". |
specificity |
The Specificity that will determine the threshold score for assignment. |
batch |
The maximum number of sequences to be assigned per batch. Bigger batches demand more memory. |
Value
A table containing the taxonomic assignment and the score to each sequence.
split_taxa
Description
Split the taxonomic assinment into 7 taxa: Domain, Phylum, Class, Order, Family and Specie.
Usage
split_taxa(taxonomy)
Arguments
taxonomy |
The taxonomy object produced by tagmeFromFasta or tagmeFromDADA2 functions. |
Value
A data frame with 7 columns: Domain, Phylum, Class, Order, Family and Specie, describing the taxonmy for each sequence. This data frame can be used as input for phyloseq::tax_table().
summarize.by.level
Description
Sum the sequences that belong to the same taxon.
Usage
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". |
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.
